From 8b42a941a426685ea96687f81deb20929d973adc Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 2 Jun 2022 15:27:13 +0300
Subject: [PATCH 01/56] [GRAPE-126] Added creation of an empty output and empty
 ibd chunks logging

---
 scripts/postprocess_ersa.py        |  5 +++++
 scripts/transform_ibis_segments.py | 15 +++++++++------
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/scripts/postprocess_ersa.py b/scripts/postprocess_ersa.py
index 67f7d956..7a26b9f9 100644
--- a/scripts/postprocess_ersa.py
+++ b/scripts/postprocess_ersa.py
@@ -90,6 +90,11 @@ def read_ersa(ersa_path):
     ibd = read_ibis(ibd_path)
     ersa = read_ersa(ersa_path)
 
+    if ibd.empty or ersa.empty:
+        logging.error("ersa postprocess input is empty")
+        with open(output_path, "w"):  # create empty output to avoid error
+            quit()
+
     logging.info(f'ibd shape: {ibd.shape[0]}, ersa shape: {ersa.shape[0]}')
 
     relatives = ibd.merge(ersa, how='outer', left_index=True, right_index=True)
diff --git a/scripts/transform_ibis_segments.py b/scripts/transform_ibis_segments.py
index eee588de..f8a6ffec 100644
--- a/scripts/transform_ibis_segments.py
+++ b/scripts/transform_ibis_segments.py
@@ -26,7 +26,7 @@ def process_chunk_with_hash(data: pandas.DataFrame, denominator: int, dest_dir:
         dest_file = os.path.join(dest_dir, f'{bucket_id}.tsv')
         group.drop('bucket_id', inplace=True, axis='columns')
         group.to_csv(dest_file, index=False, header=None, sep='\t', mode='a')
-    
+
 
 def split_by_id(input_ibd: str, samples_count: int, dest_dir: str):
     names = [
@@ -43,13 +43,16 @@ def split_by_id(input_ibd: str, samples_count: int, dest_dir: str):
         'error_count',
         'error_density'
     ]
-    read_chunksize = int(1e+6) 
+    read_chunksize = int(1e+6)
     samples_chunksize = 2000
     denominator = samples_count // samples_chunksize + 1
-    
+
     for i, chunk in enumerate(pandas.read_csv(input_ibd, header=None, names=names, sep='\t', chunksize=read_chunksize)):
-        process_chunk_with_hash(chunk, denominator, dest_dir)
-        logging.info(f'Chunk {i} of size {read_chunksize} was written to {dest_dir} and split into {denominator} buckets')
+        if not chunk.empty:
+            process_chunk_with_hash(chunk, denominator, dest_dir)
+            logging.info(f'Chunk {i} of size {chunksize} was written to {output_ibd}')
+        else:
+            logging.info('Empty chunk')
 
 
 if __name__ == '__main__':
@@ -77,4 +80,4 @@ def split_by_id(input_ibd: str, samples_count: int, dest_dir: str):
     print(snakemake.log)
     logging.basicConfig(filename=snakemake.log[0], level=logging.DEBUG, format='%(levelname)s:%(asctime)s %(message)s')
 
-    split_by_id(ibd, samples_count, bucket_dir)
\ No newline at end of file
+    split_by_id(ibd, samples_count, bucket_dir)

From c13854bcd83b88c5019884b63631aa83ccd91592 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 2 Jun 2022 17:24:25 +0300
Subject: [PATCH 02/56] [GRAPE-126] Fixed ersa and germline falling when empty
 ibd

---
 rules/relatives.smk           | 2 ++
 rules/relatives_ibis.smk      | 1 +
 rules/relatives_ibis_king.smk | 1 +
 3 files changed, 4 insertions(+)

diff --git a/rules/relatives.smk b/rules/relatives.smk
index 2f56517a..46952a80 100644
--- a/rules/relatives.smk
+++ b/rules/relatives.smk
@@ -106,6 +106,7 @@ rule germline:
         "benchmarks/germline/germline-{chrom}.txt"
     shell:
         """
+        touch {output}
         germline -input ped/imputed_chr{wildcards.chrom}.ped cm/chr{wildcards.chrom}.cm.map -min_m 2.5 -err_hom 2 -err_het 1 -output germline/chr{wildcards.chrom}.germline |& tee {log}
         # TODO: germline returns some length in BP instead of cM - clean up is needed
         set +e
@@ -153,6 +154,7 @@ rule ersa:
         ersa_t = config['ibis_seg_len']    # min length of segment to be considered in segment aggregation
     shell:
         """
+        touch {output}
         ersa --avuncular-adj -ci --alpha {params.alpha} --dmax 14 -t {params.ersa_t} -l {params.ersa_l} -th {params.ersa_th} {input.ibd} -o {output} |& tee {log}
         """
 
diff --git a/rules/relatives_ibis.smk b/rules/relatives_ibis.smk
index a662b48a..ce0ce40a 100644
--- a/rules/relatives_ibis.smk
+++ b/rules/relatives_ibis.smk
@@ -91,6 +91,7 @@ rule ersa:
         r = '--nomask ' + '-r ' + str(config['ersa_r']) if config.get('weight_mask') else ''
     shell:
         """
+        touch {output}
         FILES="{input.ibd}"
         TEMPFILE=ersa/temp_relatives.tsv
         rm -f $TEMPFILE
diff --git a/rules/relatives_ibis_king.smk b/rules/relatives_ibis_king.smk
index f5505169..528600ce 100644
--- a/rules/relatives_ibis_king.smk
+++ b/rules/relatives_ibis_king.smk
@@ -131,6 +131,7 @@ rule ersa:
         r = '--nomask ' + '-r ' + str(config['ersa_r']) if config.get('weight_mask') else ''
     shell:
         """
+        touch {output}
         FILES="{input.ibd}"
         TEMPFILE=ersa/temp_relatives.tsv
         rm -f $TEMPFILE

From b68e8ba89ac0388c00b08f8e51e4febefa57ceb8 Mon Sep 17 00:00:00 2001
From: kosar <52824960+Jahysama@users.noreply.github.com>
Date: Thu, 2 Jun 2022 18:36:57 +0300
Subject: [PATCH 03/56] [GRAPE-126] Added chunk number in logging

---
 scripts/transform_ibis_segments.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/transform_ibis_segments.py b/scripts/transform_ibis_segments.py
index f8a6ffec..7c6acd2d 100644
--- a/scripts/transform_ibis_segments.py
+++ b/scripts/transform_ibis_segments.py
@@ -52,7 +52,7 @@ def split_by_id(input_ibd: str, samples_count: int, dest_dir: str):
             process_chunk_with_hash(chunk, denominator, dest_dir)
             logging.info(f'Chunk {i} of size {chunksize} was written to {output_ibd}')
         else:
-            logging.info('Empty chunk')
+            logging.info(f'Empty chunk {i}')
 
 
 if __name__ == '__main__':

From 869b1aeac42f7c629a998b57d5dd62dea0effa6c Mon Sep 17 00:00:00 2001
From: Misha Lebedev <43742053+josephkott@users.noreply.github.com>
Date: Fri, 3 Jun 2022 12:23:09 +0300
Subject: [PATCH 04/56] [GRAPE-114] Pytest with GitHub actions (#74)

---
 .github/workflows/pytest.yml          |  24 +++
 launcher.py                           |   3 +-
 test/reference_directory.py           |  53 ++++++
 test/reference_directory_content.json | 236 ++++++++++++++++++++++++++
 test/requirements.txt                 |   2 +
 test/test.py                          | 124 ++++++++++++++
 6 files changed, 441 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/pytest.yml
 create mode 100644 test/reference_directory.py
 create mode 100644 test/reference_directory_content.json
 create mode 100644 test/requirements.txt
 create mode 100644 test/test.py

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
new file mode 100644
index 00000000..f01d3820
--- /dev/null
+++ b/.github/workflows/pytest.yml
@@ -0,0 +1,24 @@
+name: Run Python Tests
+
+on:
+  pull_request:
+    branches:
+      - master
+
+  workflow_dispatch:
+
+jobs:
+  test:
+    # Self-hosted runner
+    runs-on: self-hosted
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+      - run: |
+          python -m pip install --upgrade pip
+          pip install -r test/requirements.txt
+      - run: |
+          pytest test/test.py
diff --git a/launcher.py b/launcher.py
index ad9dbb5d..7535fae4 100644
--- a/launcher.py
+++ b/launcher.py
@@ -226,6 +226,7 @@ def get_parser_args():
 
     parser.add_argument(
         '--use-bundle',
+        action='store_true',
         default=False,
         help='Download all references as single file'
     )
@@ -286,7 +287,7 @@ def get_parser_args():
         raise ValueError('If --impute is present, then --phase must also be present')
 
     if args.command != 'reference' and args.use_bundle:
-        raise ValueError('--bundle option only available for reference downloading')
+        raise ValueError('--use-bundle option only available for reference downloading')
 
     if args.num_batches > args.cores:
         raise ValueError('Number of batches is bigger than number cores, please change --num-batches value to be lower or equal --cores')
diff --git a/test/reference_directory.py b/test/reference_directory.py
new file mode 100644
index 00000000..79e77c31
--- /dev/null
+++ b/test/reference_directory.py
@@ -0,0 +1,53 @@
+import os
+import sys
+import json
+
+
+class ReferenceDirectory:
+    @staticmethod
+    def _get_valid_content_filepath():
+        """
+        Path to the JSON file with valid reference directory content. The file contains
+        relative paths of the reference files along with their content size. This data is
+        used to validate downloaded reference data instead of MD5 hash, since hashing
+        takes significant amount of time.
+        """
+
+        module = sys.modules[ReferenceDirectory.__module__]
+        return os.path.join(
+            os.path.dirname(module.__file__),
+            'reference_directory_content.json'
+        )
+
+    @staticmethod
+    def _get_content(reference_directory_path):
+        """
+        Get a content structure of the reference directory.
+        Return a dictionary of relative paths and the files content size.
+        """
+
+        content = {}
+        for root, _, filenames in os.walk(reference_directory_path):
+            for filename in filenames:
+                filepath = os.path.join(root, filename)
+                relative_path = os.path.relpath(filepath, reference_directory_path)
+                content[relative_path] = os.path.getsize(filepath)
+
+        return content
+
+    def __init__(self, path):
+        self.path = path
+        self.content = self._get_content(path)
+
+    def is_valid(self):
+        if not os.path.exists(self.path):
+            return False
+
+        with open(self._get_valid_content_filepath(), 'r') as dump_file:
+            content = json.load(dump_file)
+
+        return content == self.content
+
+    def to_json(self, filepath):
+        with open(filepath, 'w') as dump_file:
+            json.dump(self.content, dump_file)
diff --git a/test/reference_directory_content.json b/test/reference_directory_content.json
new file mode 100644
index 00000000..b3848451
--- /dev/null
+++ b/test/reference_directory_content.json
@@ -0,0 +1,236 @@
+{
+    "hg38ToHg19.over.chain.gz": 1234991,
+    "ref.tar.gz": 18582485368,
+    "human_g1k_v37.fasta": 3153506519,
+    "refined_mf.simmap": 37825969,
+    "human_g1k_v37.fasta.dict": 8565,
+    "human_g1k_v37.fasta.fai": 2746,
+    "tables/genetic_map_hg19_withX.txt.gz": 52604097,
+    "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 38311349,
+    "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.rec": 11990378,
+    "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.rec": 8133736,
+    "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 24055058,
+    "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.rec": 5333239,
+    "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.rec": 18748262,
+    "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.rec": 8986449,
+    "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7103848,
+    "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.rec": 15930558,
+    "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 62417364,
+    "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.erate": 5100768,
+    "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.erate": 10084296,
+    "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.erate": 12608679,
+    "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 22305046,
+    "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.rec": 10323624,
+    "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 53933547,
+    "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.rec": 19977178,
+    "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.erate": 6542601,
+    "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.rec": 12796530,
+    "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.rec": 13002403,
+    "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.erate": 10823924,
+    "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 43535076,
+    "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.erate": 9367158,
+    "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.erate": 7795170,
+    "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 13790079,
+    "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.rec": 5607306,
+    "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 64747353,
+    "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8870302,
+    "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 14180633,
+    "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 53969062,
+    "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.erate": 11215304,
+    "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.rec": 14808668,
+    "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 49898243,
+    "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4849094,
+    "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 26760805,
+    "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.erate": 11840195,
+    "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.rec": 12444581,
+    "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.erate": 3357273,
+    "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 47512655,
+    "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.erate": 2177020,
+    "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.erate": 7511242,
+    "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 30134079,
+    "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.rec": 6484945,
+    "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 37911148,
+    "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.rec": 3369556,
+    "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.rec": 3623064,
+    "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4587630,
+    "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 25359752,
+    "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4292160,
+    "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4199447,
+    "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.rec": 14004332,
+    "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8016272,
+    "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 19251181,
+    "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8244282,
+    "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 47076989,
+    "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.rec": 17217197,
+    "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7489748,
+    "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 40557920,
+    "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 28019449,
+    "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 26667176,
+    "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 37873939,
+    "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.rec": 17125067,
+    "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7075199,
+    "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.erate": 3632971,
+    "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.erate": 2278008,
+    "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.erate": 5791665,
+    "Refined_genetic_map_b37/sexavg_chr15.txt": 1258453,
+    "Refined_genetic_map_b37/female_chr18.txt": 1011472,
+    "Refined_genetic_map_b37/female_chr2.txt": 2891338,
+    "Refined_genetic_map_b37/female_chr20.txt": 872520,
+    "Refined_genetic_map_b37/sexavg_chr18.txt": 1239257,
+    "Refined_genetic_map_b37/sexavg_chr2.txt": 3543171,
+    "Refined_genetic_map_b37/male_chr13.txt": 1291268,
+    "Refined_genetic_map_b37/sexavg_chr7.txt": 2351268,
+    "Refined_genetic_map_b37/male_chr18.txt": 1020424,
+    "Refined_genetic_map_b37/sexavg_chr9.txt": 1933065,
+    "Refined_genetic_map_b37/male_chr5.txt": 2050633,
+    "Refined_genetic_map_b37/male_chr12.txt": 1720053,
+    "Refined_genetic_map_b37/male_chr1.txt": 2870866,
+    "Refined_genetic_map_b37/male_chr14.txt": 1105016,
+    "Refined_genetic_map_b37/male_chr7.txt": 1936732,
+    "Refined_genetic_map_b37/sexavg_chr14.txt": 1340059,
+    "Refined_genetic_map_b37/sexavg_chr21.txt": 593610,
+    "Refined_genetic_map_b37/female_chr6.txt": 2046772,
+    "Refined_genetic_map_b37/female_chr8.txt": 1716612,
+    "Refined_genetic_map_b37/sexavg_chr13.txt": 1562619,
+    "Refined_genetic_map_b37/female_chr3.txt": 2308988,
+    "Refined_genetic_map_b37/male_chr22.txt": 530705,
+    "Refined_genetic_map_b37/male_chr4.txt": 2227330,
+    "Refined_genetic_map_b37/sexavg_chr17.txt": 1130464,
+    "Refined_genetic_map_b37/male_chr11.txt": 1649392,
+    "Refined_genetic_map_b37/female_chr7.txt": 1916280,
+    "Refined_genetic_map_b37/male_chr21.txt": 484768,
+    "Refined_genetic_map_b37/sexavg_chr16.txt": 1298614,
+    "Refined_genetic_map_b37/sexavg_chr12.txt": 2082020,
+    "Refined_genetic_map_b37/sexavg_chr8.txt": 2109709,
+    "Refined_genetic_map_b37/male_chr20.txt": 878898,
+    "Refined_genetic_map_b37/sexavg_chr5.txt": 2486464,
+    "Refined_genetic_map_b37/female_chr13.txt": 1279710,
+    "Refined_genetic_map_b37/male_chr17.txt": 931727,
+    "Refined_genetic_map_b37/female_chr10.txt": 1740905,
+    "Refined_genetic_map_b37/male_chr9.txt": 1590811,
+    "Refined_genetic_map_b37/sexavg_chr4.txt": 2698295,
+    "Refined_genetic_map_b37/female_chr19.txt": 622606,
+    "Refined_genetic_map_b37/female_chr16.txt": 1059105,
+    "Refined_genetic_map_b37/female_chrX.txt": 722638,
+    "Refined_genetic_map_b37/male_chr3.txt": 2334037,
+    "Refined_genetic_map_b37/female_chr5.txt": 2027853,
+    "Refined_genetic_map_b37/male_chr8.txt": 1739140,
+    "Refined_genetic_map_b37/male_chr19.txt": 626614,
+    "Refined_genetic_map_b37/male_chr2.txt": 2922829,
+    "Refined_genetic_map_b37/female_chr1.txt": 2842911,
+    "Refined_genetic_map_b37/female_chr11.txt": 1632476,
+    "Refined_genetic_map_b37/male_chr6.txt": 2071334,
+    "Refined_genetic_map_b37/sexavg_chr11.txt": 1995252,
+    "Refined_genetic_map_b37/sexavg_chr1.txt": 3482091,
+    "Refined_genetic_map_b37/female_chr17.txt": 922224,
+    "Refined_genetic_map_b37/sexavg_chr20.txt": 1069161,
+    "Refined_genetic_map_b37/female_chr14.txt": 1098139,
+    "Refined_genetic_map_b37/sexavg_chr10.txt": 2129730,
+    "Refined_genetic_map_b37/female_chr4.txt": 2201049,
+    "Refined_genetic_map_b37/female_chr12.txt": 1702643,
+    "Refined_genetic_map_b37/female_chr22.txt": 529559,
+    "Refined_genetic_map_b37/male_chr10.txt": 1761400,
+    "Refined_genetic_map_b37/sexavg_chr22.txt": 647332,
+    "Refined_genetic_map_b37/female_chr21.txt": 484000,
+    "Refined_genetic_map_b37/sexavg_chr3.txt": 2831085,
+    "Refined_genetic_map_b37/female_chr9.txt": 1574488,
+    "Refined_genetic_map_b37/male_chr15.txt": 1037574,
+    "Refined_genetic_map_b37/sexavg_chr6.txt": 2511850,
+    "Refined_genetic_map_b37/male_chr16.txt": 1070803,
+    "Refined_genetic_map_b37/sexavg_chr19.txt": 762575,
+    "Refined_genetic_map_b37/female_chr15.txt": 1029613,
+    "genetic_map_b37/genetic_map_chr2_combined_b37.txt": 10975990,
+    "genetic_map_b37/genetic_map_chr4_combined_b37.txt": 8006964,
+    "genetic_map_b37/genetic_map_chr3_combined_b37.txt": 8476265,
+    "genetic_map_b37/genetic_map_chr12_combined_b37.txt": 6151965,
+    "genetic_map_b37/genetic_map_chr11_combined_b37.txt": 6357243,
+    "genetic_map_b37/genetic_map_chr19_combined_b37.txt": 1776710,
+    "genetic_map_b37/genetic_map_chr17_combined_b37.txt": 2831582,
+    "genetic_map_b37/genetic_map_chr13_combined_b37.txt": 5138675,
+    "genetic_map_b37/genetic_map_chr8_combined_b37.txt": 7219386,
+    "genetic_map_b37/genetic_map_chr16_combined_b37.txt": 3513867,
+    "genetic_map_b37/genetic_map_chr7_combined_b37.txt": 6945309,
+    "genetic_map_b37/genetic_map_chr22_combined_b37.txt": 1686715,
+    "genetic_map_b37/genetic_map_chr10_combined_b37.txt": 6813552,
+    "genetic_map_b37/genetic_map_chr9_combined_b37.txt": 5950834,
+    "genetic_map_b37/genetic_map_chr18_combined_b37.txt": 3846050,
+    "genetic_map_b37/genetic_map_chr1_combined_b37.txt": 9798376,
+    "genetic_map_b37/genetic_map_chr5_combined_b37.txt": 8141057,
+    "genetic_map_b37/genetic_map_chr14_combined_b37.txt": 4057540,
+    "genetic_map_b37/genetic_map_chr6_combined_b37.txt": 8798602,
+    "genetic_map_b37/genetic_map_chr21_combined_b37.txt": 1669990,
+    "genetic_map_b37/genetic_map_chr20_combined_b37.txt": 3086646,
+    "genetic_map_b37/genetic_map_chr15_combined_b37.txt": 3511911,
+    "1000genome/allele_info/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.only_rs.biallelic.tab": 11321122455,
+    "1000genome/bcf/1000genome_chr16.bcf.csi": 65752,
+    "1000genome/bcf/1000genome_chr11.bcf.csi": 110787,
+    "1000genome/bcf/1000genome_chr17.bcf": 435200400,
+    "1000genome/bcf/1000genome_chr3.bcf.csi": 168707,
+    "1000genome/bcf/1000genome_chr4.bcf": 1121333806,
+    "1000genome/bcf/1000genome_chr4.bcf.csi": 157244,
+    "1000genome/bcf/1000genome_chr22.bcf": 215215786,
+    "1000genome/bcf/1000genome_chr11.bcf": 768825694,
+    "1000genome/bcf/1000genome_chr6.bcf": 1004197908,
+    "1000genome/bcf/1000genome_chr6.bcf.csi": 140879,
+    "1000genome/bcf/1000genome_chr21.bcf": 219664560,
+    "1000genome/bcf/1000genome_chr20.bcf": 342468968,
+    "1000genome/bcf/1000genome_chr22.bcf.csi": 28595,
+    "1000genome/bcf/1000genome_chr18.bcf": 437894679,
+    "1000genome/bcf/1000genome_chr2.bcf": 1314061281,
+    "1000genome/bcf/1000genome_chr17.bcf.csi": 65069,
+    "1000genome/bcf/1000genome_chr10.bcf": 776442213,
+    "1000genome/bcf/1000genome_chr21.bcf.csi": 28824,
+    "1000genome/bcf/1000genome_chr14.bcf.csi": 73760,
+    "1000genome/bcf/1000genome_chr12.bcf.csi": 110839,
+    "1000genome/bcf/1000genome_chr7.bcf.csi": 132897,
+    "1000genome/bcf/1000genome_chr19.bcf.csi": 49732,
+    "1000genome/bcf/1000genome_chr15.bcf": 458839209,
+    "1000genome/bcf/1000genome_chr9.bcf.csi": 100696,
+    "1000genome/bcf/1000genome_chr8.bcf.csi": 120454,
+    "1000genome/bcf/1000genome_chr10.bcf.csi": 111843,
+    "1000genome/bcf/1000genome_chr5.bcf.csi": 148879,
+    "1000genome/bcf/1000genome_chr1.bcf.csi": 182048,
+    "1000genome/bcf/1000genome_chr13.bcf": 559093113,
+    "1000genome/bcf/1000genome_chr7.bcf": 910616163,
+    "1000genome/bcf/1000genome_chr5.bcf": 991043474,
+    "1000genome/bcf/1000genome_chr16.bcf": 495726157,
+    "1000genome/bcf/1000genome_chr2.bcf.csi": 200334,
+    "1000genome/bcf/1000genome_chr3.bcf": 1108026434,
+    "1000genome/bcf/1000genome_chr15.bcf.csi": 66132,
+    "1000genome/bcf/1000genome_chr13.bcf.csi": 79552,
+    "1000genome/bcf/1000genome_chr9.bcf": 674181206,
+    "1000genome/bcf/1000genome_chr1.bcf": 1218805649,
+    "1000genome/bcf/1000genome_chr14.bcf": 507978610,
+    "1000genome/bcf/1000genome_chr18.bcf.csi": 62374,
+    "1000genome/bcf/1000genome_chr12.bcf": 743123551,
+    "1000genome/bcf/1000genome_chr8.bcf": 862933354,
+    "1000genome/bcf/1000genome_chr20.bcf.csi": 49191,
+    "1000genome/bcf/1000genome_chr19.bcf": 361013775,
+    "1000genome/affymetrix_chip/all.vcf.gz": 782884333,
+    "1000genome/affymetrix_chip/all.vcf.gz.tbi": 2038827,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr5.txt": 7303158,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr12.txt": 5710169,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr16.txt": 3167749,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr7.txt": 6219422,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr6.txt": 7918268,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr22.txt": 1540819,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr8.txt": 6416103,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr13.txt": 4687436,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr19.txt": 1593309,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chrX_par1.txt": 50520,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr18.txt": 3488316,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr1.txt": 8806085,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr4.txt": 7175980,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr20.txt": 2806690,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr2.txt": 9792987,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr3.txt": 7589745,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr21.txt": 1517797,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr10.txt": 6251004,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr14.txt": 3688036,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr15.txt": 3196892,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr17.txt": 2538845,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chrX_par2.txt": 6854,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr11.txt": 5829848,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chr9.txt": 5297717,
+    "genetic_map_GRCh37/genetic_map_GRCh37_chrX.txt": 3023467
+}
diff --git a/test/requirements.txt b/test/requirements.txt
new file mode 100644
index 00000000..77d0d9cf
--- /dev/null
+++ b/test/requirements.txt
@@ -0,0 +1,2 @@
+docker
+pytest
diff --git a/test/test.py b/test/test.py
new file mode 100644
index 00000000..c1349bea
--- /dev/null
+++ b/test/test.py
@@ -0,0 +1,124 @@
+import os
+import pytest
+import docker
+import csv
+import shutil
+
+from datetime import datetime
+from reference_directory import ReferenceDirectory
+
+
+HOME_DIRECTORY = os.path.expanduser('~')
+
+GRAPE_DOCKERFILE = 'containers/snakemake/Dockerfile'
+GRAPE_IMAGE_TAG = 'genx_relatives:latest'
+
+REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref')
+CONTAINER_REFERENCE_DIRECTORY = '/media/ref'
+CONTAINER_WORKING_DIRECTORY = '/media/data'
+METRICS_FILEPATH = 'results/metrics.tsv'
+
+
+def _get_download_reference_command(reference_directory):
+    return f'launcher.py reference --use-bundle --ref-directory {reference_directory} ' \
+            '--phase --impute --real-run'
+
+
+def _get_simulate_command(reference_directory, working_directory):
+    return f'launcher.py simulate --ref-directory {reference_directory} --cores 8 ' \
+           f'--directory {working_directory} --flow ibis --assembly hg37 --seed 42 --real-run'
+
+
+def _read_metrics_file(filepath):
+    metrics = {}
+    with open(filepath, 'r') as metrics_file:
+        reader = csv.DictReader(metrics_file, delimiter='\t')
+        for row in reader:
+            degree = row['True Degree']
+            metrics[degree] = {
+                'Precision': float(row['Precision']),
+                'Recall': float(row['Recall'])
+            }
+
+    return metrics
+
+
+@pytest.fixture
+def docker_client():
+    client = docker.from_env()
+    return client
+
+
+@pytest.fixture
+def grape_image(docker_client):
+    """
+    Build Docker image to evaluate tests.
+    """
+
+    docker_client.images.build(
+        path='.', dockerfile=GRAPE_DOCKERFILE, tag=GRAPE_IMAGE_TAG,
+        rm=True, container_limits={'memory': 8 * 1024 * 1024 * 1024}
+    )
+
+    yield docker_client.images.get(GRAPE_IMAGE_TAG)
+
+    # Fixture teardown to remove GRAPE Docker image
+    docker_client.images.remove(GRAPE_IMAGE_TAG, force=True, noprune=False)
+
+
+@pytest.fixture
+def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
+    reference_directory = ReferenceDirectory(REFERENCE_DIRECTORY)
+
+    if not reference_directory.is_valid():
+        command = _get_download_reference_command(CONTAINER_REFERENCE_DIRECTORY)
+        volumes = {
+            reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'rw'}
+        }
+
+        docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=command, volumes=volumes)
+
+    return reference_directory
+
+
+@pytest.fixture
+def working_directory():
+    utc_timestamp = datetime.utcnow().strftime("%Y%m%d-%H%M%S-utc")
+    working_directory_name = '-'.join('simultation-ibis', utc_timestamp)
+    working_directory_path = os.path.join(HOME_DIRECTORY, working_directory_name)
+
+    yield working_directory_path
+
+    # Fixture teardown to remove working directory
+    shutil.rmtree(working_directory_path)
+
+
+@pytest.fixture
+def simulate_command():
+    return _get_simulate_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY);
+
+
+def test_simulation(docker_client, grape_image, reference_directory, working_directory, simulate_command):
+    working_directory = os.path.join(HOME_DIRECTORY, 'simulation-ibis')
+    volumes = {
+        reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
+        working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'}
+    }
+
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
+
+    # Read file result with simulation metrics
+    metrics = _read_metrics_file(os.path.join(working_directory, METRICS_FILEPATH))
+
+    # Validate simultation metrics
+    assert metrics['1']['Recall'] > 0.99 and metrics['1']['Precision'] > 0.99
+    assert metrics['2']['Recall'] > 0.99 and metrics['2']['Precision'] > 0.99
+    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.99
+
+    assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
+    assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95
+    assert metrics['6']['Recall'] > 0.80 and metrics['6']['Precision'] > 0.90
+
+    assert metrics['7']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+    assert metrics['8']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+    assert metrics['9']['Recall'] > 0 and metrics['1']['Precision'] > 0.9

From cc63beaf915414a0b54844cd7d4a39db68b9c49f Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Fri, 3 Jun 2022 15:34:28 +0300
Subject: [PATCH 05/56] edited empty output file creation

---
 scripts/postprocess_ersa.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/postprocess_ersa.py b/scripts/postprocess_ersa.py
index 7a26b9f9..3e5a6eea 100644
--- a/scripts/postprocess_ersa.py
+++ b/scripts/postprocess_ersa.py
@@ -92,8 +92,8 @@ def read_ersa(ersa_path):
 
     if ibd.empty or ersa.empty:
         logging.error("ersa postprocess input is empty")
-        with open(output_path, "w"):  # create empty output to avoid error
-            quit()
+        open(output_path, "w").close()  # create empty output to avoid error
+        quit()
 
     logging.info(f'ibd shape: {ibd.shape[0]}, ersa shape: {ersa.shape[0]}')
 

From 19624d0b9513685b54a24010d8cf463e0e3da1fe Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Fri, 3 Jun 2022 15:39:20 +0300
Subject: [PATCH 06/56] edited chunks logging

---
 scripts/transform_ibis_segments.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/transform_ibis_segments.py b/scripts/transform_ibis_segments.py
index 7c6acd2d..158845f2 100644
--- a/scripts/transform_ibis_segments.py
+++ b/scripts/transform_ibis_segments.py
@@ -50,9 +50,9 @@ def split_by_id(input_ibd: str, samples_count: int, dest_dir: str):
     for i, chunk in enumerate(pandas.read_csv(input_ibd, header=None, names=names, sep='\t', chunksize=read_chunksize)):
         if not chunk.empty:
             process_chunk_with_hash(chunk, denominator, dest_dir)
-            logging.info(f'Chunk {i} of size {chunksize} was written to {output_ibd}')
+            logging.info(f'Chunk {i} of size {read_chunksize} was written to {dest_dir} and split into {denominator} buckets')
         else:
-            logging.info(f'Empty chunk {i}')
+            logging.info(f'Empty chunk was written to {output_ibd}')
 
 
 if __name__ == '__main__':

From 11b01584ae04a74ccc01ed32803726bf51566cad Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Mon, 6 Jun 2022 12:34:30 +0300
Subject: [PATCH 07/56] [GRAPE-126] Changed logging of empty ibd

Co-authored-by: Misha Lebedev <43742053+josephkott@users.noreply.github.com>
---
 scripts/transform_ibis_segments.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/transform_ibis_segments.py b/scripts/transform_ibis_segments.py
index 158845f2..0541b225 100644
--- a/scripts/transform_ibis_segments.py
+++ b/scripts/transform_ibis_segments.py
@@ -52,7 +52,7 @@ def split_by_id(input_ibd: str, samples_count: int, dest_dir: str):
             process_chunk_with_hash(chunk, denominator, dest_dir)
             logging.info(f'Chunk {i} of size {read_chunksize} was written to {dest_dir} and split into {denominator} buckets')
         else:
-            logging.info(f'Empty chunk was written to {output_ibd}')
+            logging.info(f'No IBD segments were found in {input_ibd}. Nothing was written to {dest_dir}')
 
 
 if __name__ == '__main__':

From 454937363019047b5a4fa8b3966a3a4190380b7a Mon Sep 17 00:00:00 2001
From: Misha Lebedev <43742053+josephkott@users.noreply.github.com>
Date: Wed, 8 Jun 2022 16:26:46 +0300
Subject: [PATCH 08/56] [GRAPE-114] run pytest only for develop -> master PR,
 forks do not run pytest as well (#76)

---
 .github/workflows/pytest.yml       | 7 +++++--
 .github/workflows/verify_files.yml | 6 +++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index f01d3820..4dc0347d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -2,8 +2,8 @@ name: Run Python Tests
 
 on:
   pull_request:
-    branches:
-      - master
+    branches: [ master ]
+    types: [ opened ]
 
   workflow_dispatch:
 
@@ -11,6 +11,9 @@ jobs:
   test:
     # Self-hosted runner
     runs-on: self-hosted
+    if: |
+      !github.event.pull_request.head.repo.fork &&
+      github.head_ref == 'develop'
 
     steps:
       - uses: actions/checkout@v3
diff --git a/.github/workflows/verify_files.yml b/.github/workflows/verify_files.yml
index 06b708bf..c7e8d342 100644
--- a/.github/workflows/verify_files.yml
+++ b/.github/workflows/verify_files.yml
@@ -3,16 +3,16 @@ name: verify-files
 on:
   schedule:
     - cron: "0 0 * * *"
-    
+
   workflow_dispatch:
 
 jobs:
   verify-files:
     runs-on: ubuntu-latest
-    
+
     steps:
       - uses: actions/checkout@v2
-      
+
       - name: Setup python
         run: "python -m pip install pyyaml"
 

From 8df314782236cf21eefa9c5aa963096c67611a08 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 9 Jun 2022 12:36:27 +0300
Subject: [PATCH 09/56] added phased reference dir path

---
 config.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/config.yaml b/config.yaml
index fd4742e4..b50fd159 100644
--- a/config.yaml
+++ b/config.yaml
@@ -36,6 +36,8 @@ reference:
     url: https://ftp-trace.ncbi.nih.gov/hapmap/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz
     filesize: 37730100
     md5: 1bc10a34d985e68e1f38ceb137b87929
+  phased_ref:
+    file: 1000genome/phased/chr{chrom}.phased.vcf.gz
   vcfRef:
     file: 1000genome/bcf/1000genome_chr{chrom}.bcf
     url: https://dataset1000genomes.blob.core.windows.net/dataset/release/20130502/supporting/bcf_files/ALL.chr$chrom.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf
@@ -107,3 +109,4 @@ reference:
   picard:
     file: picard.jar
     url: https://github.com/broadinstitute/picard/releases/download/2.26.2/picard.jar
+

From 6fb6ef5859075dcf1f485e7e88c7b1ff1f90d232 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 9 Jun 2022 12:37:06 +0300
Subject: [PATCH 10/56] [GRAPE-127] Moved rule intersec to reference
 downloading

---
 workflows/pedsim/Snakefile | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/workflows/pedsim/Snakefile b/workflows/pedsim/Snakefile
index 3fe1267a..64a4efc6 100644
--- a/workflows/pedsim/Snakefile
+++ b/workflows/pedsim/Snakefile
@@ -6,6 +6,7 @@ use_simulated_ibd = config['use_simulated_ibd'] if 'use_simulated_ibd' in config
 
 REF_DIR            = config['ref_dir']
 GRCH37_FASTA       = join(REF_DIR, config['reference']['GRCh37_fasta']['file'])
+PHASED_VCF         = join(REF_DIR, config['reference']['phased_ref']['file'])
 GENETIC_MAP        = join(REF_DIR, config['reference']['GENETIC_MAP']['file'])
 GENETIC_MAP_GRCH37 = join(REF_DIR, config['reference']['genetic_map_GRCh37']['file'])
 REF_VCF            = join(REF_DIR, config['reference']['vcfRef']['file'])
@@ -44,22 +45,9 @@ rule all:
         'results/accuracy.png'
 
 
-rule intersect:
-    input:
-        hd_genotype_chip=AFFYMETRIX_CHIP,
-        vcfRef=REF_VCF
-    output: 'pedsim/phased/chr{chrom}.phased.vcf.gz'
-    conda: '../../envs/bcftools.yaml'
-    shell:
-        """
-            bcftools isec -n=2 -w1 -r {wildcards.chrom} \
-             -O z -o {output} {input.vcfRef} {input.hd_genotype_chip}
-        """
-
-
 rule merge_background:
     input:
-        data=expand('pedsim/phased/chr{chrom}.phased.vcf.gz', chrom=CHROMOSOMES),
+        data=expand(PHASED_VCF, chrom=CHROMOSOMES),
         eu=config['sim_samples_file']
     output:
         'pedsim/phased/background.vcf.gz'

From 3151aac0cb3e6f881360719271b9182de36f172d Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 9 Jun 2022 12:39:21 +0300
Subject: [PATCH 11/56] [GRAPE-127] Moved rule intersec from pedsim workflow

---
 workflows/reference/Snakefile | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/workflows/reference/Snakefile b/workflows/reference/Snakefile
index 4e198519..c3b1c61f 100644
--- a/workflows/reference/Snakefile
+++ b/workflows/reference/Snakefile
@@ -16,6 +16,8 @@ CMMAP              = join(REF_DIR, config["reference"]["cmmap"]["file"])
 SITE_1000GENOME    = join(REF_DIR, config["reference"]["SITE_1000GENOME"]["file"])
 AFFYMETRIX_CHIP    = join(REF_DIR, config["reference"]["affymetrix_chip"]["file"])
 PEDSIM_MAP         = join(REF_DIR, config["reference"]["pedsim_map"]["file"])
+REF_VCF            = join(REF_DIR, config['reference']['vcfRef']['file'])
+PHASED_VCF         = join(REF_DIR, config['reference']['phased_ref']['file'])
 
 GRCH37_FASTA_url            = config["reference"]["GRCh37_fasta"]["url"]
 GRCH37_FASTA_md5            = config["reference"]["GRCh37_fasta"]["md5"]
@@ -75,7 +77,8 @@ if need_phase or need_imputation:
             pedsim_map = PEDSIM_MAP,
             affymetrix_chip = AFFYMETRIX_CHIP,
             vcfRef = expand(REF_VCF, chrom=CHROMOSOMES),
-            refHaps = expand(REF_HAPS, chrom=CHROMOSOMES)
+            refHaps = expand(REF_HAPS, chrom=CHROMOSOMES),
+            phased_vcf = expand(PHASED_VCF, chrom=CHROMOSOMES)
 else:
     rule all:
         input:
@@ -325,6 +328,18 @@ rule download_affymetrix_chip:
             wget "{AFFYMETRIX_CHIP_url}.tbi{DATASET_KEY}" -O {AFFYMETRIX_CHIP}.tbi --tries 50 -c  |& tee -a {log}
         """
 
+rule intersect:
+    input:
+        hd_genotype_chip=AFFYMETRIX_CHIP,
+        vcfRef=REF_VCF
+    output: PHASED_VCF
+    conda: '../../envs/bcftools.yaml'
+    shell:
+        """
+            bcftools isec -n=2 -w1 -r {wildcards.chrom} \
+             -O z -o {output} {input.vcfRef} {input.hd_genotype_chip}
+        """
+
 
 rule download_pedsim_map:
     output:
@@ -350,4 +365,3 @@ rule download_pedsim_map:
             done
             rm -f {REF_DIR}/{PEDSIM_MAP_basename} |& tee -a {log}
         """
-        

From 428adbd38a46a76a492a8d657033007b2983ba59 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 16 Jun 2022 11:46:46 +0300
Subject: [PATCH 12/56] [GRAPE-127]does not work without 'True'

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6e20824c..7805b3ed 100644
--- a/README.md
+++ b/README.md
@@ -62,7 +62,7 @@ This way is faster, since all the post-processing procedures have been already p
 
 ```bash
 docker run --rm -it -v /media:/media -v /etc/localtime:/etc/localtime:ro \
-    genx_relatives:latest launcher.py reference --use-bundle \
+    genx_relatives:latest launcher.py reference --use-bundle True\
         --ref-directory /media/ref --phase --impute --real-run
 ```
 

From b46693c17057bd7deb1b233b4d61f934d055533c Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 16 Jun 2022 11:48:12 +0300
Subject: [PATCH 13/56] added phased_vcf in rule all, unpacked ref_test inside
 archive

---
 workflows/bundle/Snakefile | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/workflows/bundle/Snakefile b/workflows/bundle/Snakefile
index a4f55715..ae2314a9 100644
--- a/workflows/bundle/Snakefile
+++ b/workflows/bundle/Snakefile
@@ -12,6 +12,7 @@ CMMAP              = join(REF_DIR, config["reference"]["cmmap"]["file"])
 SITE_1000GENOME    = join(REF_DIR, config["reference"]["SITE_1000GENOME"]["file"])
 AFFYMETRIX_CHIP    = join(REF_DIR, config["reference"]["affymetrix_chip"]["file"])
 PEDSIM_MAP         = join(REF_DIR, config["reference"]["pedsim_map"]["file"])
+PHASED_VCF         = join(REF_DIR, config['reference']['phased_ref']['file'])
 
 full = config['phase'] or config['impute']
 
@@ -34,7 +35,8 @@ if full:
             pedsim_map = PEDSIM_MAP,
             affymetrix_chip = AFFYMETRIX_CHIP,
             vcfRef = expand(REF_VCF, chrom=CHROMOSOMES),
-            refHaps = expand(REF_HAPS, chrom=CHROMOSOMES)
+            refHaps = expand(REF_HAPS, chrom=CHROMOSOMES),
+            phased_vcf = expand(PHASED_VCF, chrom=CHROMOSOMES)
         conda:
             "../../envs/download.yaml"
         log:
@@ -48,6 +50,9 @@ if full:
                     exit 1
                 fi
                 tar -xzvf {REF_DIR}/{BUNDLE_basename} -C {REF_DIR} |& tee -a {log}
+                mv -bfv ref_test/* {REF_DIR}
+                rm -rf ref_test
+                find -name "*~" -delete
                 rm -f {REF_DIR}/{BUNDLE_basename} |& tee -a {log}
             """
 else:

From 6dd75d79d39c62a8936334b99ca209f6255afecc Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 16 Jun 2022 11:49:51 +0300
Subject: [PATCH 14/56] [GRAPE-127] edited new bundle link, md5, file_size

---
 config.yaml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/config.yaml b/config.yaml
index b50fd159..b80db750 100644
--- a/config.yaml
+++ b/config.yaml
@@ -98,9 +98,9 @@ reference:
     md5: 39e6e8620d616362875f2538eae2f279
   bundle:
     file: ref.tar.gz
-    url: https://bioinformatics.file.core.windows.net/bundles/ref.tar.gz
-    filesize: 18582485368
-    md5: 67278f83139f375e22bd56544d523fa3
+    url: https://bioinformatics.file.core.windows.net/bundles/ref_v2.tar.gz
+    filesize: 19411373184
+    md5: 8043d70ff7dbdc35e67c7d3728bb7ad8
   bundle_min:
     file: ref_min.tar.gz
     url: https://bioinformatics.file.core.windows.net/bundles/ref_min.tar.gz
@@ -109,4 +109,3 @@ reference:
   picard:
     file: picard.jar
     url: https://github.com/broadinstitute/picard/releases/download/2.26.2/picard.jar
-

From 5cb7d353c23f8938862434747b7ccaa7aaba8a11 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Sun, 19 Jun 2022 16:02:19 +0300
Subject: [PATCH 15/56] [GRAPE-127] Fixed bundle archive issue

---
 README.md                             |   2 +-
 config.yaml                           |   4 +-
 test/reference_directory_content.json | 543 +++++++++++++++-----------
 workflows/bundle/Snakefile            |   3 -
 4 files changed, 312 insertions(+), 240 deletions(-)

diff --git a/README.md b/README.md
index 7805b3ed..5cf8f5c2 100644
--- a/README.md
+++ b/README.md
@@ -62,7 +62,7 @@ This way is faster, since all the post-processing procedures have been already p
 
 ```bash
 docker run --rm -it -v /media:/media -v /etc/localtime:/etc/localtime:ro \
-    genx_relatives:latest launcher.py reference --use-bundle True\
+    genx_relatives:latest launcher.py reference --use-bundle\
         --ref-directory /media/ref --phase --impute --real-run
 ```
 
diff --git a/config.yaml b/config.yaml
index b80db750..17b7a76c 100644
--- a/config.yaml
+++ b/config.yaml
@@ -99,8 +99,8 @@ reference:
   bundle:
     file: ref.tar.gz
     url: https://bioinformatics.file.core.windows.net/bundles/ref_v2.tar.gz
-    filesize: 19411373184
-    md5: 8043d70ff7dbdc35e67c7d3728bb7ad8
+    filesize: 19411359855
+    md5: 300fa3e768b677958a2b8e270115c6d9
   bundle_min:
     file: ref_min.tar.gz
     url: https://bioinformatics.file.core.windows.net/bundles/ref_min.tar.gz
diff --git a/test/reference_directory_content.json b/test/reference_directory_content.json
index b3848451..baecd3d8 100644
--- a/test/reference_directory_content.json
+++ b/test/reference_directory_content.json
@@ -1,236 +1,311 @@
 {
-    "hg38ToHg19.over.chain.gz": 1234991,
-    "ref.tar.gz": 18582485368,
-    "human_g1k_v37.fasta": 3153506519,
-    "refined_mf.simmap": 37825969,
-    "human_g1k_v37.fasta.dict": 8565,
-    "human_g1k_v37.fasta.fai": 2746,
-    "tables/genetic_map_hg19_withX.txt.gz": 52604097,
-    "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 38311349,
-    "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.rec": 11990378,
-    "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.rec": 8133736,
-    "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 24055058,
-    "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.rec": 5333239,
-    "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.rec": 18748262,
-    "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.rec": 8986449,
-    "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7103848,
-    "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.rec": 15930558,
-    "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 62417364,
-    "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.erate": 5100768,
-    "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.erate": 10084296,
-    "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.erate": 12608679,
-    "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 22305046,
-    "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.rec": 10323624,
-    "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 53933547,
-    "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.rec": 19977178,
-    "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.erate": 6542601,
-    "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.rec": 12796530,
-    "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.rec": 13002403,
-    "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.erate": 10823924,
-    "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 43535076,
-    "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.erate": 9367158,
-    "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.erate": 7795170,
-    "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 13790079,
-    "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.rec": 5607306,
-    "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 64747353,
-    "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8870302,
-    "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 14180633,
-    "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 53969062,
-    "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.erate": 11215304,
-    "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.rec": 14808668,
-    "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 49898243,
-    "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4849094,
-    "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 26760805,
-    "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.erate": 11840195,
-    "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.rec": 12444581,
-    "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.erate": 3357273,
-    "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 47512655,
-    "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.erate": 2177020,
-    "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.erate": 7511242,
-    "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 30134079,
-    "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.rec": 6484945,
-    "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 37911148,
-    "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.rec": 3369556,
-    "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.rec": 3623064,
-    "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4587630,
-    "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 25359752,
-    "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4292160,
-    "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4199447,
-    "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.rec": 14004332,
-    "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8016272,
-    "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 19251181,
-    "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8244282,
-    "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 47076989,
-    "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.rec": 17217197,
-    "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7489748,
-    "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 40557920,
-    "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 28019449,
-    "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 26667176,
-    "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 37873939,
-    "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.rec": 17125067,
-    "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7075199,
-    "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.erate": 3632971,
-    "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.erate": 2278008,
-    "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.erate": 5791665,
-    "Refined_genetic_map_b37/sexavg_chr15.txt": 1258453,
-    "Refined_genetic_map_b37/female_chr18.txt": 1011472,
-    "Refined_genetic_map_b37/female_chr2.txt": 2891338,
-    "Refined_genetic_map_b37/female_chr20.txt": 872520,
-    "Refined_genetic_map_b37/sexavg_chr18.txt": 1239257,
-    "Refined_genetic_map_b37/sexavg_chr2.txt": 3543171,
-    "Refined_genetic_map_b37/male_chr13.txt": 1291268,
-    "Refined_genetic_map_b37/sexavg_chr7.txt": 2351268,
-    "Refined_genetic_map_b37/male_chr18.txt": 1020424,
-    "Refined_genetic_map_b37/sexavg_chr9.txt": 1933065,
-    "Refined_genetic_map_b37/male_chr5.txt": 2050633,
-    "Refined_genetic_map_b37/male_chr12.txt": 1720053,
-    "Refined_genetic_map_b37/male_chr1.txt": 2870866,
-    "Refined_genetic_map_b37/male_chr14.txt": 1105016,
-    "Refined_genetic_map_b37/male_chr7.txt": 1936732,
-    "Refined_genetic_map_b37/sexavg_chr14.txt": 1340059,
-    "Refined_genetic_map_b37/sexavg_chr21.txt": 593610,
-    "Refined_genetic_map_b37/female_chr6.txt": 2046772,
-    "Refined_genetic_map_b37/female_chr8.txt": 1716612,
-    "Refined_genetic_map_b37/sexavg_chr13.txt": 1562619,
-    "Refined_genetic_map_b37/female_chr3.txt": 2308988,
-    "Refined_genetic_map_b37/male_chr22.txt": 530705,
-    "Refined_genetic_map_b37/male_chr4.txt": 2227330,
-    "Refined_genetic_map_b37/sexavg_chr17.txt": 1130464,
-    "Refined_genetic_map_b37/male_chr11.txt": 1649392,
-    "Refined_genetic_map_b37/female_chr7.txt": 1916280,
-    "Refined_genetic_map_b37/male_chr21.txt": 484768,
-    "Refined_genetic_map_b37/sexavg_chr16.txt": 1298614,
-    "Refined_genetic_map_b37/sexavg_chr12.txt": 2082020,
-    "Refined_genetic_map_b37/sexavg_chr8.txt": 2109709,
-    "Refined_genetic_map_b37/male_chr20.txt": 878898,
-    "Refined_genetic_map_b37/sexavg_chr5.txt": 2486464,
-    "Refined_genetic_map_b37/female_chr13.txt": 1279710,
-    "Refined_genetic_map_b37/male_chr17.txt": 931727,
-    "Refined_genetic_map_b37/female_chr10.txt": 1740905,
-    "Refined_genetic_map_b37/male_chr9.txt": 1590811,
-    "Refined_genetic_map_b37/sexavg_chr4.txt": 2698295,
-    "Refined_genetic_map_b37/female_chr19.txt": 622606,
-    "Refined_genetic_map_b37/female_chr16.txt": 1059105,
-    "Refined_genetic_map_b37/female_chrX.txt": 722638,
-    "Refined_genetic_map_b37/male_chr3.txt": 2334037,
-    "Refined_genetic_map_b37/female_chr5.txt": 2027853,
-    "Refined_genetic_map_b37/male_chr8.txt": 1739140,
-    "Refined_genetic_map_b37/male_chr19.txt": 626614,
-    "Refined_genetic_map_b37/male_chr2.txt": 2922829,
-    "Refined_genetic_map_b37/female_chr1.txt": 2842911,
-    "Refined_genetic_map_b37/female_chr11.txt": 1632476,
-    "Refined_genetic_map_b37/male_chr6.txt": 2071334,
-    "Refined_genetic_map_b37/sexavg_chr11.txt": 1995252,
-    "Refined_genetic_map_b37/sexavg_chr1.txt": 3482091,
-    "Refined_genetic_map_b37/female_chr17.txt": 922224,
-    "Refined_genetic_map_b37/sexavg_chr20.txt": 1069161,
-    "Refined_genetic_map_b37/female_chr14.txt": 1098139,
-    "Refined_genetic_map_b37/sexavg_chr10.txt": 2129730,
-    "Refined_genetic_map_b37/female_chr4.txt": 2201049,
-    "Refined_genetic_map_b37/female_chr12.txt": 1702643,
-    "Refined_genetic_map_b37/female_chr22.txt": 529559,
-    "Refined_genetic_map_b37/male_chr10.txt": 1761400,
-    "Refined_genetic_map_b37/sexavg_chr22.txt": 647332,
-    "Refined_genetic_map_b37/female_chr21.txt": 484000,
-    "Refined_genetic_map_b37/sexavg_chr3.txt": 2831085,
-    "Refined_genetic_map_b37/female_chr9.txt": 1574488,
-    "Refined_genetic_map_b37/male_chr15.txt": 1037574,
-    "Refined_genetic_map_b37/sexavg_chr6.txt": 2511850,
-    "Refined_genetic_map_b37/male_chr16.txt": 1070803,
-    "Refined_genetic_map_b37/sexavg_chr19.txt": 762575,
-    "Refined_genetic_map_b37/female_chr15.txt": 1029613,
-    "genetic_map_b37/genetic_map_chr2_combined_b37.txt": 10975990,
-    "genetic_map_b37/genetic_map_chr4_combined_b37.txt": 8006964,
-    "genetic_map_b37/genetic_map_chr3_combined_b37.txt": 8476265,
-    "genetic_map_b37/genetic_map_chr12_combined_b37.txt": 6151965,
-    "genetic_map_b37/genetic_map_chr11_combined_b37.txt": 6357243,
-    "genetic_map_b37/genetic_map_chr19_combined_b37.txt": 1776710,
-    "genetic_map_b37/genetic_map_chr17_combined_b37.txt": 2831582,
-    "genetic_map_b37/genetic_map_chr13_combined_b37.txt": 5138675,
-    "genetic_map_b37/genetic_map_chr8_combined_b37.txt": 7219386,
-    "genetic_map_b37/genetic_map_chr16_combined_b37.txt": 3513867,
-    "genetic_map_b37/genetic_map_chr7_combined_b37.txt": 6945309,
-    "genetic_map_b37/genetic_map_chr22_combined_b37.txt": 1686715,
-    "genetic_map_b37/genetic_map_chr10_combined_b37.txt": 6813552,
-    "genetic_map_b37/genetic_map_chr9_combined_b37.txt": 5950834,
-    "genetic_map_b37/genetic_map_chr18_combined_b37.txt": 3846050,
-    "genetic_map_b37/genetic_map_chr1_combined_b37.txt": 9798376,
-    "genetic_map_b37/genetic_map_chr5_combined_b37.txt": 8141057,
-    "genetic_map_b37/genetic_map_chr14_combined_b37.txt": 4057540,
-    "genetic_map_b37/genetic_map_chr6_combined_b37.txt": 8798602,
-    "genetic_map_b37/genetic_map_chr21_combined_b37.txt": 1669990,
-    "genetic_map_b37/genetic_map_chr20_combined_b37.txt": 3086646,
-    "genetic_map_b37/genetic_map_chr15_combined_b37.txt": 3511911,
-    "1000genome/allele_info/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.only_rs.biallelic.tab": 11321122455,
-    "1000genome/bcf/1000genome_chr16.bcf.csi": 65752,
-    "1000genome/bcf/1000genome_chr11.bcf.csi": 110787,
-    "1000genome/bcf/1000genome_chr17.bcf": 435200400,
-    "1000genome/bcf/1000genome_chr3.bcf.csi": 168707,
-    "1000genome/bcf/1000genome_chr4.bcf": 1121333806,
-    "1000genome/bcf/1000genome_chr4.bcf.csi": 157244,
-    "1000genome/bcf/1000genome_chr22.bcf": 215215786,
-    "1000genome/bcf/1000genome_chr11.bcf": 768825694,
-    "1000genome/bcf/1000genome_chr6.bcf": 1004197908,
-    "1000genome/bcf/1000genome_chr6.bcf.csi": 140879,
-    "1000genome/bcf/1000genome_chr21.bcf": 219664560,
-    "1000genome/bcf/1000genome_chr20.bcf": 342468968,
-    "1000genome/bcf/1000genome_chr22.bcf.csi": 28595,
-    "1000genome/bcf/1000genome_chr18.bcf": 437894679,
-    "1000genome/bcf/1000genome_chr2.bcf": 1314061281,
-    "1000genome/bcf/1000genome_chr17.bcf.csi": 65069,
-    "1000genome/bcf/1000genome_chr10.bcf": 776442213,
-    "1000genome/bcf/1000genome_chr21.bcf.csi": 28824,
-    "1000genome/bcf/1000genome_chr14.bcf.csi": 73760,
-    "1000genome/bcf/1000genome_chr12.bcf.csi": 110839,
-    "1000genome/bcf/1000genome_chr7.bcf.csi": 132897,
-    "1000genome/bcf/1000genome_chr19.bcf.csi": 49732,
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+  "1000genome/phased/chr4.phased.vcf.gz": 48325709,
+  "1000genome/phased/chr22.phased.vcf.gz": 9760009,
+  "1000genome/phased/chr16.phased.vcf.gz": 23843771,
+  "1000genome/phased/chr12.phased.vcf.gz": 36597898,
+  "1000genome/phased/chr6.phased.vcf.gz": 48740971,
+  "1000genome/phased/chr18.phased.vcf.gz": 22832638,
+  "1000genome/phased/chr15.phased.vcf.gz": 22677321,
+  "Refined_genetic_map_b37/sexavg_chr11.txt": 1995252,
+  "Refined_genetic_map_b37/sexavg_chr19.txt": 762575,
+  "Refined_genetic_map_b37/female_chr21.txt": 484000,
+  "Refined_genetic_map_b37/sexavg_chr9.txt": 1933065,
+  "Refined_genetic_map_b37/sexavg_chr10.txt": 2129730,
+  "Refined_genetic_map_b37/male_chr2.txt": 2922829,
+  "Refined_genetic_map_b37/sexavg_chr14.txt": 1340059,
+  "Refined_genetic_map_b37/female_chr14.txt": 1098139,
+  "Refined_genetic_map_b37/female_chr6.txt": 2046772,
+  "Refined_genetic_map_b37/female_chr22.txt": 529559,
+  "Refined_genetic_map_b37/female_chr18.txt": 1011472,
+  "Refined_genetic_map_b37/sexavg_chr21.txt": 593610,
+  "Refined_genetic_map_b37/male_chr11.txt": 1649392,
+  "Refined_genetic_map_b37/male_chr22.txt": 530705,
+  "Refined_genetic_map_b37/male_chr16.txt": 1070803,
+  "Refined_genetic_map_b37/female_chr15.txt": 1029613,
+  "Refined_genetic_map_b37/female_chr10.txt": 1740905,
+  "Refined_genetic_map_b37/sexavg_chr20.txt": 1069161,
+  "Refined_genetic_map_b37/sexavg_chr16.txt": 1298614,
+  "Refined_genetic_map_b37/sexavg_chr17.txt": 1130464,
+  "Refined_genetic_map_b37/female_chr17.txt": 922224,
+  "Refined_genetic_map_b37/female_chr4.txt": 2201049,
+  "Refined_genetic_map_b37/sexavg_chr2.txt": 3543171,
+  "Refined_genetic_map_b37/sexavg_chr8.txt": 2109709,
+  "Refined_genetic_map_b37/male_chr12.txt": 1720053,
+  "Refined_genetic_map_b37/female_chr2.txt": 2891338,
+  "Refined_genetic_map_b37/male_chr6.txt": 2071334,
+  "Refined_genetic_map_b37/female_chr11.txt": 1632476,
+  "Refined_genetic_map_b37/male_chr10.txt": 1761400,
+  "Refined_genetic_map_b37/sexavg_chr22.txt": 647332,
+  "Refined_genetic_map_b37/male_chr5.txt": 2050633,
+  "Refined_genetic_map_b37/female_chr8.txt": 1716612,
+  "Refined_genetic_map_b37/sexavg_chr4.txt": 2698295,
+  "Refined_genetic_map_b37/male_chr13.txt": 1291268,
+  "Refined_genetic_map_b37/male_chr1.txt": 2870866,
+  "Refined_genetic_map_b37/male_chr19.txt": 626614,
+  "Refined_genetic_map_b37/female_chr7.txt": 1916280,
+  "Refined_genetic_map_b37/female_chr16.txt": 1059105,
+  "Refined_genetic_map_b37/male_chr8.txt": 1739140,
+  "Refined_genetic_map_b37/male_chr3.txt": 2334037,
+  "Refined_genetic_map_b37/male_chr18.txt": 1020424,
+  "Refined_genetic_map_b37/male_chr17.txt": 931727,
+  "Refined_genetic_map_b37/male_chr4.txt": 2227330,
+  "Refined_genetic_map_b37/male_chr15.txt": 1037574,
+  "Refined_genetic_map_b37/sexavg_chr3.txt": 2831085,
+  "Refined_genetic_map_b37/sexavg_chr18.txt": 1239257,
+  "Refined_genetic_map_b37/male_chr9.txt": 1590811,
+  "Refined_genetic_map_b37/female_chr19.txt": 622606,
+  "Refined_genetic_map_b37/female_chr13.txt": 1279710,
+  "Refined_genetic_map_b37/female_chr5.txt": 2027853,
+  "Refined_genetic_map_b37/female_chr3.txt": 2308988,
+  "Refined_genetic_map_b37/sexavg_chr12.txt": 2082020,
+  "Refined_genetic_map_b37/female_chr12.txt": 1702643,
+  "Refined_genetic_map_b37/female_chr9.txt": 1574488,
+  "Refined_genetic_map_b37/male_chr14.txt": 1105016,
+  "Refined_genetic_map_b37/male_chr20.txt": 878898,
+  "Refined_genetic_map_b37/sexavg_chr7.txt": 2351268,
+  "Refined_genetic_map_b37/female_chrX.txt": 722638,
+  "Refined_genetic_map_b37/sexavg_chr13.txt": 1562619,
+  "Refined_genetic_map_b37/sexavg_chr5.txt": 2486464,
+  "Refined_genetic_map_b37/male_chr7.txt": 1936732,
+  "Refined_genetic_map_b37/female_chr20.txt": 872520,
+  "Refined_genetic_map_b37/female_chr1.txt": 2842911,
+  "Refined_genetic_map_b37/sexavg_chr15.txt": 1258453,
+  "Refined_genetic_map_b37/sexavg_chr1.txt": 3482091,
+  "Refined_genetic_map_b37/male_chr21.txt": 484768,
+  "Refined_genetic_map_b37/sexavg_chr6.txt": 2511850,
+  "tables/genetic_map_hg19_withX.txt.gz": 52604097
 }
diff --git a/workflows/bundle/Snakefile b/workflows/bundle/Snakefile
index ae2314a9..aad02a8a 100644
--- a/workflows/bundle/Snakefile
+++ b/workflows/bundle/Snakefile
@@ -50,9 +50,6 @@ if full:
                     exit 1
                 fi
                 tar -xzvf {REF_DIR}/{BUNDLE_basename} -C {REF_DIR} |& tee -a {log}
-                mv -bfv ref_test/* {REF_DIR}
-                rm -rf ref_test
-                find -name "*~" -delete
                 rm -f {REF_DIR}/{BUNDLE_basename} |& tee -a {log}
             """
 else:

From 9b339b78db50864fe8d06e20eaa8add0ecde6fcd Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Mon, 20 Jun 2022 17:53:46 +0300
Subject: [PATCH 16/56] [GRAPE-127] Added space

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 5cf8f5c2..6e20824c 100644
--- a/README.md
+++ b/README.md
@@ -62,7 +62,7 @@ This way is faster, since all the post-processing procedures have been already p
 
 ```bash
 docker run --rm -it -v /media:/media -v /etc/localtime:/etc/localtime:ro \
-    genx_relatives:latest launcher.py reference --use-bundle\
+    genx_relatives:latest launcher.py reference --use-bundle \
         --ref-directory /media/ref --phase --impute --real-run
 ```
 

From d1b408b8be203bf1fdbd771a87abcc8698597b23 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Mon, 20 Jun 2022 18:34:50 +0300
Subject: [PATCH 17/56] [GRAPE-127] Added 2 more spaces for intent

---
 test/reference_directory_content.json | 618 +++++++++++++-------------
 1 file changed, 309 insertions(+), 309 deletions(-)

diff --git a/test/reference_directory_content.json b/test/reference_directory_content.json
index baecd3d8..42bb7b2a 100644
--- a/test/reference_directory_content.json
+++ b/test/reference_directory_content.json
@@ -1,311 +1,311 @@
 {
-  "stat_file.txt": 36010,
-  "refined_mf.simmap": 37825969,
-  "human_g1k_v37.fasta.dict": 8901,
-  "human_g1k_v37.fasta.fai": 2746,
-  "human_g1k_v37.fasta": 3153506519,
-  "hg38ToHg19.over.chain.gz": 1234991,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chrX_par2.txt": 6854,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr22.txt": 1540819,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr8.txt": 6416103,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr18.txt": 3488316,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr9.txt": 5297717,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr6.txt": 7918268,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr7.txt": 6219422,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr4.txt": 7175980,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr14.txt": 3688036,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chrX_par1.txt": 50520,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr13.txt": 4687436,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr20.txt": 2806690,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr15.txt": 3196892,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr5.txt": 7303158,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr2.txt": 9792987,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr17.txt": 2538845,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chrX.txt": 3023467,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr3.txt": 7589745,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr10.txt": 6251004,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr12.txt": 5710169,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr21.txt": 1517797,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr11.txt": 5829848,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr16.txt": 3167749,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr1.txt": 8806085,
-  "genetic_map_GRCh37/genetic_map_GRCh37_chr19.txt": 1593309,
-  "logs/ref/make_refHaps2.log": 13263,
-  "logs/ref/download_vcfRef19.log": 443794,
-  "logs/ref/download_vcfRef12.log": 919904,
-  "logs/ref/make_refHaps15.log": 8278,
-  "logs/ref/make_refHaps13.log": 9064,
-  "logs/ref/make_refHaps12.log": 9987,
-  "logs/ref/download_vcfRef13.log": 691383,
-  "logs/ref/make_refHaps11.log": 10246,
-  "logs/ref/download_vcfRef5.log": 1228827,
-  "logs/ref/download_vcfRef22.log": 264697,
-  "logs/ref/make_refHaps9.log": 9586,
-  "logs/ref/download_GRCh37_fasta.log": 1341146,
-  "logs/ref/download_vcfRef20.log": 424459,
-  "logs/ref/make_refHaps20.log": 7623,
-  "logs/ref/make_refHaps18.log": 8276,
-  "logs/ref/make_refHaps21.log": 6962,
-  "logs/ref/download_affymetrix_chip.log": 1183838,
-  "logs/ref/make_refHaps5.log": 11292,
-  "logs/ref/download_cmmap.log": 79637,
-  "logs/ref/download_vcfRef2.log": 1631950,
-  "logs/ref/make_refHaps10.log": 10381,
-  "logs/ref/download_vcfRef17.log": 538059,
-  "logs/ref/make_refHaps17.log": 8146,
-  "logs/ref/download_vcfRef4.log": 1386261,
-  "logs/ref/download_vcfRef21.log": 269864,
-  "logs/ref/make_refHaps16.log": 8540,
-  "logs/ref/download_vcfRef10.log": 960493,
-  "logs/ref/download_vcfRef3.log": 1374454,
-  "logs/ref/download_vcfRef1.log": 1509402,
-  "logs/ref/download_vcfRef15.log": 566927,
-  "logs/ref/make_refHaps6.log": 11817,
-  "logs/ref/make_refHaps22.log": 6820,
-  "logs/ref/download_SITE_1000GENOME.log": 2227871,
-  "logs/ref/download_vcfRef6.log": 1242173,
-  "logs/ref/make_refHaps8.log": 10763,
-  "logs/ref/download_vcfRef9.log": 835802,
-  "logs/ref/make_refHaps4.log": 12469,
-  "logs/ref/create_fasta_dict.log": 29807,
-  "logs/ref/download_pedsim_map.log": 78161,
-  "logs/ref/download_vcfRef18.log": 542083,
-  "logs/ref/download_vcfRef16.log": 613328,
-  "logs/ref/make_refHaps14.log": 8666,
-  "logs/ref/download_GENETIC_MAP.log": 78705,
-  "logs/ref/download_lift_chain.log": 2390,
-  "logs/ref/make_refHaps19.log": 7755,
-  "logs/ref/download_vcfRef7.log": 1129236,
-  "logs/ref/make_refHaps3.log": 12211,
-  "logs/ref/download_vcfRef8.log": 1068912,
-  "logs/ref/download_vcfRef14.log": 629031,
-  "logs/ref/download_genetic_map_GRCh37.log": 57314,
-  "logs/ref/make_refHaps7.log": 11028,
-  "logs/ref/make_refHaps1.log": 12868,
-  "logs/ref/download_vcfRef11.log": 951992,
-  "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.erate": 11840195,
-  "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.rec": 13002403,
-  "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4587630,
-  "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8870302,
-  "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.rec": 11990378,
-  "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.erate": 5791665,
-  "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.rec": 3369556,
-  "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7103848,
-  "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.erate": 6542601,
-  "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.rec": 19977178,
-  "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8016272,
-  "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.rec": 15930558,
-  "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.rec": 17217197,
-  "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 13790079,
-  "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 40557920,
-  "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.rec": 14004332,
-  "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 38311349,
-  "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 14180633,
-  "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 47076989,
-  "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 53969062,
-  "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.erate": 12608679,
-  "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 62417364,
-  "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 37873939,
-  "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.rec": 5333239,
-  "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.rec": 14808668,
-  "Minimac/22.1000g.Phase3.v5.With.Parameter.Estimates.erate": 2177020,
-  "Minimac/7.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 47512655,
-  "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 53933545,
-  "Minimac/10.1000g.Phase3.v5.With.Parameter.Estimates.rec": 12796530,
-  "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.erate": 7511242,
-  "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.rec": 8986449,
-  "Minimac/1.1000g.Phase3.v5.With.Parameter.Estimates.rec": 18748262,
-  "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 26760805,
-  "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 30134079,
-  "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.erate": 8244282,
-  "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.rec": 8133736,
-  "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 22305046,
-  "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 49898243,
-  "Minimac/13.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 28019449,
-  "Minimac/2.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 64747353,
-  "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 25359752,
-  "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7489748,
-  "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.erate": 7795170,
-  "Minimac/15.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 26667176,
-  "Minimac/9.1000g.Phase3.v5.With.Parameter.Estimates.rec": 10323624,
-  "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.erate": 10823925,
-  "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 24055058,
-  "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4292160,
-  "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.erate": 3357273,
-  "Minimac/20.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 19251181,
-  "Minimac/18.1000g.Phase3.v5.With.Parameter.Estimates.rec": 7075199,
-  "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.erate": 3632971,
-  "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4199447,
-  "Minimac/3.1000g.Phase3.v5.With.Parameter.Estimates.rec": 17125067,
-  "Minimac/19.1000g.Phase3.v5.With.Parameter.Estimates.rec": 5607306,
-  "Minimac/14.1000g.Phase3.v5.With.Parameter.Estimates.erate": 5100768,
-  "Minimac/4.1000g.Phase3.v5.With.Parameter.Estimates.erate": 11215304,
-  "Minimac/6.1000g.Phase3.v5.With.Parameter.Estimates.erate": 10084296,
-  "Minimac/8.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 43535076,
-  "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.rec": 3623064,
-  "Minimac/16.1000g.Phase3.v5.With.Parameter.Estimates.erate": 4849094,
-  "Minimac/17.1000g.Phase3.v5.With.Parameter.Estimates.rec": 6484945,
-  "Minimac/5.1000g.Phase3.v5.With.Parameter.Estimates.erate": 9367158,
-  "Minimac/21.1000g.Phase3.v5.With.Parameter.Estimates.erate": 2278008,
-  "Minimac/11.1000g.Phase3.v5.With.Parameter.Estimates.rec": 12444581,
-  "Minimac/12.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz": 37911148,
-  "genetic_map_b37/genetic_map_chr4_combined_b37.txt": 8006964,
-  "genetic_map_b37/genetic_map_chr11_combined_b37.txt": 6357243,
-  "genetic_map_b37/genetic_map_chr20_combined_b37.txt": 3086646,
-  "genetic_map_b37/genetic_map_chr22_combined_b37.txt": 1686715,
-  "genetic_map_b37/genetic_map_chr3_combined_b37.txt": 8476265,
-  "genetic_map_b37/genetic_map_chr2_combined_b37.txt": 10975990,
-  "genetic_map_b37/genetic_map_chr19_combined_b37.txt": 1776710,
-  "genetic_map_b37/genetic_map_chr16_combined_b37.txt": 3513867,
-  "genetic_map_b37/genetic_map_chr13_combined_b37.txt": 5138675,
-  "genetic_map_b37/genetic_map_chr21_combined_b37.txt": 1669990,
-  "genetic_map_b37/genetic_map_chr6_combined_b37.txt": 8798602,
-  "genetic_map_b37/genetic_map_chr5_combined_b37.txt": 8141057,
-  "genetic_map_b37/genetic_map_chr8_combined_b37.txt": 7219386,
-  "genetic_map_b37/genetic_map_chr1_combined_b37.txt": 9798376,
-  "genetic_map_b37/genetic_map_chr14_combined_b37.txt": 4057540,
-  "genetic_map_b37/genetic_map_chr15_combined_b37.txt": 3511911,
-  "genetic_map_b37/genetic_map_chr9_combined_b37.txt": 5950834,
-  "genetic_map_b37/genetic_map_chr18_combined_b37.txt": 3846050,
-  "genetic_map_b37/genetic_map_chr12_combined_b37.txt": 6151965,
-  "genetic_map_b37/genetic_map_chr7_combined_b37.txt": 6945309,
-  "genetic_map_b37/genetic_map_chr10_combined_b37.txt": 6813552,
-  "genetic_map_b37/genetic_map_chr17_combined_b37.txt": 2831582,
-  "1000genome/bcf/1000genome_chr14.bcf": 511866177,
-  "1000genome/bcf/1000genome_chr20.bcf.csi": 49213,
-  "1000genome/bcf/1000genome_chr8.bcf.csi": 120255,
-  "1000genome/bcf/1000genome_chr19.bcf.csi": 49637,
-  "1000genome/bcf/1000genome_chr18.bcf": 441331298,
-  "1000genome/bcf/1000genome_chr9.bcf": 679190908,
-  "1000genome/bcf/1000genome_chr21.bcf.csi": 28497,
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+    "genetic_map_b37/genetic_map_chr21_combined_b37.txt": 1669990,
+    "genetic_map_b37/genetic_map_chr6_combined_b37.txt": 8798602,
+    "genetic_map_b37/genetic_map_chr5_combined_b37.txt": 8141057,
+    "genetic_map_b37/genetic_map_chr8_combined_b37.txt": 7219386,
+    "genetic_map_b37/genetic_map_chr1_combined_b37.txt": 9798376,
+    "genetic_map_b37/genetic_map_chr14_combined_b37.txt": 4057540,
+    "genetic_map_b37/genetic_map_chr15_combined_b37.txt": 3511911,
+    "genetic_map_b37/genetic_map_chr9_combined_b37.txt": 5950834,
+    "genetic_map_b37/genetic_map_chr18_combined_b37.txt": 3846050,
+    "genetic_map_b37/genetic_map_chr12_combined_b37.txt": 6151965,
+    "genetic_map_b37/genetic_map_chr7_combined_b37.txt": 6945309,
+    "genetic_map_b37/genetic_map_chr10_combined_b37.txt": 6813552,
+    "genetic_map_b37/genetic_map_chr17_combined_b37.txt": 2831582,
+    "1000genome/bcf/1000genome_chr14.bcf": 511866177,
+    "1000genome/bcf/1000genome_chr20.bcf.csi": 49213,
+    "1000genome/bcf/1000genome_chr8.bcf.csi": 120255,
+    "1000genome/bcf/1000genome_chr19.bcf.csi": 49637,
+    "1000genome/bcf/1000genome_chr18.bcf": 441331298,
+    "1000genome/bcf/1000genome_chr9.bcf": 679190908,
+    "1000genome/bcf/1000genome_chr21.bcf.csi": 28497,
+    "1000genome/bcf/1000genome_chr13.bcf.csi": 79468,
+    "1000genome/bcf/1000genome_chr15.bcf.csi": 65897,
+    "1000genome/bcf/1000genome_chr10.bcf": 782006214,
+    "1000genome/bcf/1000genome_chr18.bcf.csi": 62201,
+    "1000genome/bcf/1000genome_chr1.bcf.csi": 181942,
+    "1000genome/bcf/1000genome_chr3.bcf": 1115991764,
+    "1000genome/bcf/1000genome_chr7.bcf.csi": 132950,
+    "1000genome/bcf/1000genome_chr6.bcf": 1011549295,
+    "1000genome/bcf/1000genome_chr8.bcf": 869374649,
+    "1000genome/bcf/1000genome_chr4.bcf": 1129422190,
+    "1000genome/bcf/1000genome_chr13.bcf": 563298560,
+    "1000genome/bcf/1000genome_chr7.bcf": 917324887,
+    "1000genome/bcf/1000genome_chr14.bcf.csi": 73345,
+    "1000genome/bcf/1000genome_chr22.bcf": 216932756,
+    "1000genome/bcf/1000genome_chr2.bcf.csi": 200346,
+    "1000genome/bcf/1000genome_chr16.bcf.csi": 65713,
+    "1000genome/bcf/1000genome_chr17.bcf.csi": 64962,
+    "1000genome/bcf/1000genome_chr22.bcf.csi": 28522,
+    "1000genome/bcf/1000genome_chr12.bcf": 748644151,
+    "1000genome/bcf/1000genome_chr10.bcf.csi": 111499,
+    "1000genome/bcf/1000genome_chr16.bcf": 499597061,
+    "1000genome/bcf/1000genome_chr5.bcf": 998201667,
+    "1000genome/bcf/1000genome_chr2.bcf": 1323221709,
+    "1000genome/bcf/1000genome_chr5.bcf.csi": 148630,
+    "1000genome/bcf/1000genome_chr12.bcf.csi": 110984,
+    "1000genome/bcf/1000genome_chr15.bcf": 462444925,
+    "1000genome/bcf/1000genome_chr11.bcf": 774475140,
+    "1000genome/bcf/1000genome_chr21.bcf": 221399023,
+    "1000genome/bcf/1000genome_chr17.bcf": 438721232,
+    "1000genome/bcf/1000genome_chr6.bcf.csi": 140644,
+    "1000genome/bcf/1000genome_chr11.bcf.csi": 110727,
+    "1000genome/bcf/1000genome_chr1.bcf": 1227349297,
+    "1000genome/bcf/1000genome_chr19.bcf": 363902919,
+    "1000genome/bcf/1000genome_chr4.bcf.csi": 156900,
+    "1000genome/bcf/1000genome_chr3.bcf.csi": 168525,
+    "1000genome/bcf/1000genome_chr9.bcf.csi": 100098,
+    "1000genome/bcf/1000genome_chr20.bcf": 345147207,
+    "1000genome/allele_info/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.only_rs.biallelic.tab": 11321122455,
+    "1000genome/affymetrix_chip/all.vcf.gz": 782884333,
+    "1000genome/affymetrix_chip/all.vcf.gz.tbi": 2038827,
+    "1000genome/phased/chr17.phased.vcf.gz": 17907117,
+    "1000genome/phased/chr8.phased.vcf.gz": 42117299,
+    "1000genome/phased/chr10.phased.vcf.gz": 41258805,
+    "1000genome/phased/chr1.phased.vcf.gz": 60937160,
+    "1000genome/phased/chr5.phased.vcf.gz": 47749537,
+    "1000genome/phased/chr3.phased.vcf.gz": 52814757,
+    "1000genome/phased/chr19.phased.vcf.gz": 10541897,
+    "1000genome/phased/chr14.phased.vcf.gz": 24288993,
+    "1000genome/phased/chr13.phased.vcf.gz": 29390773,
+    "1000genome/phased/chr21.phased.vcf.gz": 11000743,
+    "1000genome/phased/chr2.phased.vcf.gz": 63550469,
+    "1000genome/phased/chr20.phased.vcf.gz": 19649025,
+    "1000genome/phased/chr9.phased.vcf.gz": 36017949,
+    "1000genome/phased/chr11.phased.vcf.gz": 38583201,
+    "1000genome/phased/chr7.phased.vcf.gz": 41051395,
+    "1000genome/phased/chr4.phased.vcf.gz": 48325709,
+    "1000genome/phased/chr22.phased.vcf.gz": 9760009,
+    "1000genome/phased/chr16.phased.vcf.gz": 23843771,
+    "1000genome/phased/chr12.phased.vcf.gz": 36597898,
+    "1000genome/phased/chr6.phased.vcf.gz": 48740971,
+    "1000genome/phased/chr18.phased.vcf.gz": 22832638,
+    "1000genome/phased/chr15.phased.vcf.gz": 22677321,
+    "Refined_genetic_map_b37/sexavg_chr11.txt": 1995252,
+    "Refined_genetic_map_b37/sexavg_chr19.txt": 762575,
+    "Refined_genetic_map_b37/female_chr21.txt": 484000,
+    "Refined_genetic_map_b37/sexavg_chr9.txt": 1933065,
+    "Refined_genetic_map_b37/sexavg_chr10.txt": 2129730,
+    "Refined_genetic_map_b37/male_chr2.txt": 2922829,
+    "Refined_genetic_map_b37/sexavg_chr14.txt": 1340059,
+    "Refined_genetic_map_b37/female_chr14.txt": 1098139,
+    "Refined_genetic_map_b37/female_chr6.txt": 2046772,
+    "Refined_genetic_map_b37/female_chr22.txt": 529559,
+    "Refined_genetic_map_b37/female_chr18.txt": 1011472,
+    "Refined_genetic_map_b37/sexavg_chr21.txt": 593610,
+    "Refined_genetic_map_b37/male_chr11.txt": 1649392,
+    "Refined_genetic_map_b37/male_chr22.txt": 530705,
+    "Refined_genetic_map_b37/male_chr16.txt": 1070803,
+    "Refined_genetic_map_b37/female_chr15.txt": 1029613,
+    "Refined_genetic_map_b37/female_chr10.txt": 1740905,
+    "Refined_genetic_map_b37/sexavg_chr20.txt": 1069161,
+    "Refined_genetic_map_b37/sexavg_chr16.txt": 1298614,
+    "Refined_genetic_map_b37/sexavg_chr17.txt": 1130464,
+    "Refined_genetic_map_b37/female_chr17.txt": 922224,
+    "Refined_genetic_map_b37/female_chr4.txt": 2201049,
+    "Refined_genetic_map_b37/sexavg_chr2.txt": 3543171,
+    "Refined_genetic_map_b37/sexavg_chr8.txt": 2109709,
+    "Refined_genetic_map_b37/male_chr12.txt": 1720053,
+    "Refined_genetic_map_b37/female_chr2.txt": 2891338,
+    "Refined_genetic_map_b37/male_chr6.txt": 2071334,
+    "Refined_genetic_map_b37/female_chr11.txt": 1632476,
+    "Refined_genetic_map_b37/male_chr10.txt": 1761400,
+    "Refined_genetic_map_b37/sexavg_chr22.txt": 647332,
+    "Refined_genetic_map_b37/male_chr5.txt": 2050633,
+    "Refined_genetic_map_b37/female_chr8.txt": 1716612,
+    "Refined_genetic_map_b37/sexavg_chr4.txt": 2698295,
+    "Refined_genetic_map_b37/male_chr13.txt": 1291268,
+    "Refined_genetic_map_b37/male_chr1.txt": 2870866,
+    "Refined_genetic_map_b37/male_chr19.txt": 626614,
+    "Refined_genetic_map_b37/female_chr7.txt": 1916280,
+    "Refined_genetic_map_b37/female_chr16.txt": 1059105,
+    "Refined_genetic_map_b37/male_chr8.txt": 1739140,
+    "Refined_genetic_map_b37/male_chr3.txt": 2334037,
+    "Refined_genetic_map_b37/male_chr18.txt": 1020424,
+    "Refined_genetic_map_b37/male_chr17.txt": 931727,
+    "Refined_genetic_map_b37/male_chr4.txt": 2227330,
+    "Refined_genetic_map_b37/male_chr15.txt": 1037574,
+    "Refined_genetic_map_b37/sexavg_chr3.txt": 2831085,
+    "Refined_genetic_map_b37/sexavg_chr18.txt": 1239257,
+    "Refined_genetic_map_b37/male_chr9.txt": 1590811,
+    "Refined_genetic_map_b37/female_chr19.txt": 622606,
+    "Refined_genetic_map_b37/female_chr13.txt": 1279710,
+    "Refined_genetic_map_b37/female_chr5.txt": 2027853,
+    "Refined_genetic_map_b37/female_chr3.txt": 2308988,
+    "Refined_genetic_map_b37/sexavg_chr12.txt": 2082020,
+    "Refined_genetic_map_b37/female_chr12.txt": 1702643,
+    "Refined_genetic_map_b37/female_chr9.txt": 1574488,
+    "Refined_genetic_map_b37/male_chr14.txt": 1105016,
+    "Refined_genetic_map_b37/male_chr20.txt": 878898,
+    "Refined_genetic_map_b37/sexavg_chr7.txt": 2351268,
+    "Refined_genetic_map_b37/female_chrX.txt": 722638,
+    "Refined_genetic_map_b37/sexavg_chr13.txt": 1562619,
+    "Refined_genetic_map_b37/sexavg_chr5.txt": 2486464,
+    "Refined_genetic_map_b37/male_chr7.txt": 1936732,
+    "Refined_genetic_map_b37/female_chr20.txt": 872520,
+    "Refined_genetic_map_b37/female_chr1.txt": 2842911,
+    "Refined_genetic_map_b37/sexavg_chr15.txt": 1258453,
+    "Refined_genetic_map_b37/sexavg_chr1.txt": 3482091,
+    "Refined_genetic_map_b37/male_chr21.txt": 484768,
+    "Refined_genetic_map_b37/sexavg_chr6.txt": 2511850,
+    "tables/genetic_map_hg19_withX.txt.gz": 52604097
 }

From 8d78990d73a5dfbb06db67a78d45edff9b258b60 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Wed, 22 Jun 2022 23:33:29 +0300
Subject: [PATCH 18/56] [GRAPE-125] Added ibis-king, king-germline, aadr and
 khazar test cases

---
 test/test.py | 110 +++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 98 insertions(+), 12 deletions(-)

diff --git a/test/test.py b/test/test.py
index c1349bea..89b0fb8d 100644
--- a/test/test.py
+++ b/test/test.py
@@ -8,15 +8,20 @@
 from reference_directory import ReferenceDirectory
 
 
-HOME_DIRECTORY = os.path.expanduser('~')
+HOME_DIRECTORY = os.path.expanduser('/media/')
 
 GRAPE_DOCKERFILE = 'containers/snakemake/Dockerfile'
 GRAPE_IMAGE_TAG = 'genx_relatives:latest'
 
-REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref')
+REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref_test')
 CONTAINER_REFERENCE_DIRECTORY = '/media/ref'
 CONTAINER_WORKING_DIRECTORY = '/media/data'
+TESTING_REAL_DATA_DIRECTORY = '/media/test_data'
+KHAZAR_VCF = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'khazar314.vcf.gz')
+AADR_VCF = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr.reheaded.vcf.gz')
 METRICS_FILEPATH = 'results/metrics.tsv'
+RELATIVES_FILEPATH = 'results/relatives.tsv'
+AADR_SAMPLES_FILEPATH = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
 
 
 def _get_download_reference_command(reference_directory):
@@ -24,9 +29,19 @@ def _get_download_reference_command(reference_directory):
             '--phase --impute --real-run'
 
 
-def _get_simulate_command(reference_directory, working_directory):
+def _get_simulate_command(reference_directory, working_directory, flow):
     return f'launcher.py simulate --ref-directory {reference_directory} --cores 8 ' \
-           f'--directory {working_directory} --flow ibis --assembly hg37 --seed 42 --real-run'
+           f'--directory {working_directory} --flow {flow} --assembly hg37 --seed 42 --real-run'
+
+
+def _get_preprocess_command(reference_directory, working_directory, input_file):
+    return f'launcher.py preprocess --ref-directory {reference_directory} --cores 8 ' \
+           f'--directory {working_directory} --vcf-file {input_file} --assembly hg37 --real-run'
+
+
+def _get_find_command(reference_directory, working_directory):
+    return f'launcher.py find --ref-directory {reference_directory} --cores 8 ' \
+           f'--directory {working_directory} --flow ibis --real-run'
 
 
 def _read_metrics_file(filepath):
@@ -43,6 +58,28 @@ def _read_metrics_file(filepath):
     return metrics
 
 
+def _read_samples_file(filepath):
+    samples = {}
+    with open(filepath, 'r') as samples_file:
+        reader = csv.DictReader(samples_file)
+        for row in reader:
+            sample = row['id']
+            samples[sample] = row['date']
+
+    return samples
+
+
+def _read_relatives_file(filepath):
+    relatives = []
+    with open(filepath, 'r') as relatives_file:
+        reader = csv.DictReader(relatives_file, delimiter="\t")
+        for row in reader:
+            relative = (row['id1'], row['id2'])
+            relatives.append(relative)
+
+    return relatives
+
+
 @pytest.fixture
 def docker_client():
     client = docker.from_env()
@@ -54,7 +91,6 @@ def grape_image(docker_client):
     """
     Build Docker image to evaluate tests.
     """
-
     docker_client.images.build(
         path='.', dockerfile=GRAPE_DOCKERFILE, tag=GRAPE_IMAGE_TAG,
         rm=True, container_limits={'memory': 8 * 1024 * 1024 * 1024}
@@ -82,9 +118,14 @@ def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
 
 
 @pytest.fixture
-def working_directory():
+def test_data_directory():
+    return TESTING_REAL_DATA_DIRECTORY
+
+
+@pytest.fixture(scope="function")
+def working_directory(request):
     utc_timestamp = datetime.utcnow().strftime("%Y%m%d-%H%M%S-utc")
-    working_directory_name = '-'.join('simultation-ibis', utc_timestamp)
+    working_directory_name = '-'.join([request.param, utc_timestamp])
     working_directory_path = os.path.join(HOME_DIRECTORY, working_directory_name)
 
     yield working_directory_path
@@ -93,13 +134,32 @@ def working_directory():
     shutil.rmtree(working_directory_path)
 
 
-@pytest.fixture
-def simulate_command():
-    return _get_simulate_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY);
+@pytest.fixture(scope="function")
+def simulate_command(request):
+    return _get_simulate_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY, request.param);
+
+
+@pytest.fixture()
+def find_command():
+    return _get_find_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY);
+
+
+@pytest.fixture(scope="function")
+def preprocess_command(request):
+    return _get_preprocess_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY, request.param);
+
+
+simulation_list = [('ibis', 'simulation-ibis'),
+                   ('ibis-king', 'simulation-ibis-king'),
+                   ('germline-king --assembly hg38 --phase --impute',  # germline needs extra flags to work
+                    'simulation-germline-king')]
 
+real_data_list = [('simulation-khazar', KHAZAR_VCF),
+                  ('simulation-aadr', f'{AADR_VCF} --het-samples 0.0')]  # ancient samples have zero heterozygosity
 
+
+@pytest.mark.parametrize('simulate_command,working_directory', simulation_list, indirect=True)
 def test_simulation(docker_client, grape_image, reference_directory, working_directory, simulate_command):
-    working_directory = os.path.join(HOME_DIRECTORY, 'simulation-ibis')
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
         working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'}
@@ -113,7 +173,7 @@ def test_simulation(docker_client, grape_image, reference_directory, working_dir
     # Validate simultation metrics
     assert metrics['1']['Recall'] > 0.99 and metrics['1']['Precision'] > 0.99
     assert metrics['2']['Recall'] > 0.99 and metrics['2']['Precision'] > 0.99
-    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.99
+    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.98
 
     assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
     assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95
@@ -122,3 +182,29 @@ def test_simulation(docker_client, grape_image, reference_directory, working_dir
     assert metrics['7']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
     assert metrics['8']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
     assert metrics['9']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+
+
+@pytest.mark.parametrize('working_directory,preprocess_command', real_data_list, indirect=True)
+def test_real_data(docker_client, grape_image, reference_directory,
+                   working_directory, test_data_directory, find_command, preprocess_command):
+    volumes = {
+        reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
+        working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'},
+        test_data_directory: {'bind': TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
+    }
+
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=preprocess_command, volumes=volumes)
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=find_command, volumes=volumes)
+
+    # Read file result with relatives
+    relatives = _read_relatives_file(os.path.join(working_directory, RELATIVES_FILEPATH))
+
+    # Validate relatives
+    current_data = working_directory.split('-')[0]
+    if current_data == 'khazar':
+        num_of_relatives = len(list(relatives))
+        assert 55 >= num_of_relatives >= 57
+    elif current_data == 'aadr':
+        aadr_samples = _read_samples_file(AADR_SAMPLES_FILEPATH)
+        for relative in relatives.iterrows():
+            assert aadr_samples[relative[0]] == aadr_samples[relative[1]]

From 2d887d4456f2fe68a5df373a895faeb4e5338cde Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Wed, 22 Jun 2022 23:38:50 +0300
Subject: [PATCH 19/56] [GRAPE-125] Renamed ref and home dir back

---
 test/test.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test.py b/test/test.py
index 89b0fb8d..b7279394 100644
--- a/test/test.py
+++ b/test/test.py
@@ -8,12 +8,12 @@
 from reference_directory import ReferenceDirectory
 
 
-HOME_DIRECTORY = os.path.expanduser('/media/')
+HOME_DIRECTORY = os.path.expanduser('~')
 
 GRAPE_DOCKERFILE = 'containers/snakemake/Dockerfile'
 GRAPE_IMAGE_TAG = 'genx_relatives:latest'
 
-REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref_test')
+REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref')
 CONTAINER_REFERENCE_DIRECTORY = '/media/ref'
 CONTAINER_WORKING_DIRECTORY = '/media/data'
 TESTING_REAL_DATA_DIRECTORY = '/media/test_data'

From f2d2705760949a8b8c3102aa75e0c9bf0e7d2ac7 Mon Sep 17 00:00:00 2001
From: Jahysama <megametagross@outlook.de>
Date: Thu, 23 Jun 2022 19:10:09 +0300
Subject: [PATCH 20/56] [GRAPE-119] Made plink files merge before mapping

---
 rules/preprocessing.smk   | 132 ++++++++++++++------------------------
 scripts/remove_mapping.py |  10 ---
 2 files changed, 48 insertions(+), 94 deletions(-)
 delete mode 100644 scripts/remove_mapping.py

diff --git a/rules/preprocessing.smk b/rules/preprocessing.smk
index e1244aee..d258d586 100644
--- a/rules/preprocessing.smk
+++ b/rules/preprocessing.smk
@@ -109,7 +109,7 @@ if assembly == 'hg38':
             mem_mb=_mem_gb_for_ram_hungry_jobs() * 1024
         shell:
             '''
-               java -Xmx{params.mem_gb}g -jar /picard/picard.jar LiftoverVcf WARN_ON_MISSING_CONTIG=true MAX_RECORDS_IN_RAM=5000 I={input.vcf} O={output.vcf} CHAIN={LIFT_CHAIN} REJECT=vcf/chr{batch}_rejected.vcf.gz R={GRCH37_FASTA} |& tee -a {log}
+               java -Xmx{params.mem_gb}g -jar /picard/picard.jar LiftoverVcf WARN_ON_MISSING_CONTIG=true MAX_RECORDS_IN_RAM=5000 I={input.vcf} O={output.vcf} CHAIN={LIFT_CHAIN} REJECT=vcf/chr{wildcards.batch}_rejected.vcf.gz R={GRCH37_FASTA} |& tee -a {log}
             '''
 else:
     rule copy_liftover:
@@ -195,22 +195,40 @@ if NUM_BATCHES > 1:
             '''
 
 
-    rule ibis_mapping:
+    def get_merge_bed_input(wildcards):
+        with open('pass_batches.list','r') as list:
+            batches_left = []
+            for line in list:
+                batches_left.append(line.strip('\n'))
+            bim = ['preprocessed/{s}_data.bim'.format(s=batch) for batch in batches_left]
+            bed = ['preprocessed/{s}_data.bed'.format(s=batch) for batch in batches_left]
+            fam = ['preprocessed/{s}_data.fam'.format(s=batch) for batch in batches_left]
+        return bed + bim + fam
+
+    rule merge_bed:
         input:
-            bim=rules.convert_mapped_to_plink.output['bim']
-        params:
-            genetic_map_GRCh37=expand(GENETIC_MAP_GRCH37,chrom=CHROMOSOMES)
-        conda:
-            '../envs/ibis.yaml'
+            get_merge_bed_input
         output:
-            'preprocessed/{batch}_data_mapped.bim'
-        log:
-            'logs/ibis/run_ibis_mapping{batch}.log'
-        benchmark:
-            'benchmarks/ibis/run_ibis_mapping{batch}.txt'
+            bed='preprocessed/data.bed',
+            fam='preprocessed/data.fam',
+            bim='preprocessed/data.bim'
+        threads:
+            workflow.cores
+        conda:
+            '../envs/plink.yaml'
         shell:
             '''
-            (add-map-plink.pl -cm {input.bim} {params.genetic_map_GRCh37}> {output}) |& tee -a {log}
+            rm files_list.txt || true
+            for file in {input}
+            do
+                if [[ $file == *.fam ]]
+                then
+                    echo ${{file%.*}} >> files_list.txt
+                fi
+            done
+
+            plink --merge-list files_list.txt --make-bed --out preprocessed/data
+            rm files_list.txt
             '''
 
 
@@ -261,60 +279,6 @@ if NUM_BATCHES > 1:
             rm complete_vcf_list.txt
             '''
 
-
-    def get_merge_bed_input(wildcards):
-        with open('pass_batches.list', 'r') as list:
-            batches_left = []
-            for line in list:
-                batches_left.append(line.strip('\n'))
-        bim = ['preprocessed/{s}_data_mapped.bim'.format(s=batch) for batch in batches_left]
-        bed = ['preprocessed/{s}_data.bed'.format(s=batch) for batch in batches_left]
-        fam = ['preprocessed/{s}_data.fam'.format(s=batch) for batch in batches_left]
-        return bed + bim + fam
-
-    rule merge_bed:
-        input:
-            get_merge_bed_input
-        output:
-            bed='preprocessed/data.bed',
-            fam='preprocessed/data.fam',
-            bim_mapped='preprocessed/data_mapped.bim'
-        threads:
-            workflow.cores
-        conda:
-            '../envs/plink.yaml'
-        shell:
-            '''
-            for file in $(find preprocessed -name '*_mapped.bim')
-            do
-                new=$(echo "$file" | sed "s/_mapped//g")
-                mv "$file" "$new"
-            done
-
-            rm files_list.txt || true
-            for file in {input}
-            do
-                if [[ $file == *.fam ]]
-                then
-                    echo ${{file%.*}} >> files_list.txt
-                fi
-            done
-
-            plink --merge-list files_list.txt --make-bed --out preprocessed/data
-            mv preprocessed/data.bim preprocessed/data_mapped.bim
-            rm files_list.txt
-            '''
-
-
-    rule remove_mapping:
-        input:
-            bim_mapped = 'preprocessed/data_mapped.bim'
-        output:
-            bim='preprocessed/data.bim'
-        conda:
-            '../envs/remove_map.yaml'
-        script:
-            '../scripts/remove_mapping.py'
 else:
     rule single_batch_convert_mapped_to_plink:
         input:
@@ -337,20 +301,20 @@ else:
             '''
 
 
-    rule single_batch_ibis_mapping:
-        input:
-            bim=rules.single_batch_convert_mapped_to_plink.output['bim']
-        params:
-            genetic_map_GRCh37=expand(GENETIC_MAP_GRCH37,chrom=CHROMOSOMES)
-        conda:
-            '../envs/ibis.yaml'
-        output:
-            'preprocessed/data_mapped.bim'
-        log:
-            'logs/ibis/run_ibis_mapping_batch1.log'
-        benchmark:
-            'benchmarks/ibis/run_ibis_mapping_batch1.txt'
-        shell:
-            '''
-            (add-map-plink.pl -cm {input.bim} {params.genetic_map_GRCh37}> {output}) |& tee -a {log}
-            '''
+rule ibis_mapping:
+    input:
+        bim='preprocessed/data.bim'
+    params:
+        genetic_map_GRCh37=expand(GENETIC_MAP_GRCH37,chrom=CHROMOSOMES)
+    conda:
+        '../envs/ibis.yaml'
+    output:
+        'preprocessed/data_mapped.bim'
+    log:
+        'logs/ibis/run_ibis_mapping.log'
+    benchmark:
+        'benchmarks/ibis/run_ibis_mapping.txt'
+    shell:
+        '''
+        (add-map-plink.pl -cm {input.bim} {params.genetic_map_GRCh37}> {output}) |& tee -a {log}
+        '''
diff --git a/scripts/remove_mapping.py b/scripts/remove_mapping.py
deleted file mode 100644
index bbe95663..00000000
--- a/scripts/remove_mapping.py
+++ /dev/null
@@ -1,10 +0,0 @@
-import pandas as pd
-
-if __name__ == '__main__':
-
-  bim_mapped_path = snakemake.input['bim_mapped']
-  bim_path = snakemake.output['bim']
-
-  bim_mapped = pd.read_csv(bim_mapped_path, sep='\t', header=None)
-  bim_mapped.iloc[:, 2] = 0
-  bim_mapped.to_csv(bim_path, sep="\t", header=False, index=False)

From 6705beeff394923ff2aeafce4812be9ac8bada69 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Fri, 24 Jun 2022 01:50:59 +0300
Subject: [PATCH 21/56] [GRAPE-125] Renamed vars for a better fit

---
 test/test.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/test/test.py b/test/test.py
index b7279394..d84b0318 100644
--- a/test/test.py
+++ b/test/test.py
@@ -63,8 +63,8 @@ def _read_samples_file(filepath):
     with open(filepath, 'r') as samples_file:
         reader = csv.DictReader(samples_file)
         for row in reader:
-            sample = row['id']
-            samples[sample] = row['date']
+            sample_id = row['id']
+            samples[sample_id] = row['date']
 
     return samples
 
@@ -74,8 +74,8 @@ def _read_relatives_file(filepath):
     with open(filepath, 'r') as relatives_file:
         reader = csv.DictReader(relatives_file, delimiter="\t")
         for row in reader:
-            relative = (row['id1'], row['id2'])
-            relatives.append(relative)
+            relationship = (row['id1'], row['id2'])
+            relatives.append(relationship)
 
     return relatives
 
@@ -154,8 +154,8 @@ def preprocess_command(request):
                    ('germline-king --assembly hg38 --phase --impute',  # germline needs extra flags to work
                     'simulation-germline-king')]
 
-real_data_list = [('simulation-khazar', KHAZAR_VCF),
-                  ('simulation-aadr', f'{AADR_VCF} --het-samples 0.0')]  # ancient samples have zero heterozygosity
+real_data_list = [('realdata-khazar', KHAZAR_VCF),
+                  ('realdata-aadr', f'{AADR_VCF} --het-samples 0.0')]  # ancient samples have zero heterozygosity
 
 
 @pytest.mark.parametrize('simulate_command,working_directory', simulation_list, indirect=True)
@@ -206,5 +206,5 @@ def test_real_data(docker_client, grape_image, reference_directory,
         assert 55 >= num_of_relatives >= 57
     elif current_data == 'aadr':
         aadr_samples = _read_samples_file(AADR_SAMPLES_FILEPATH)
-        for relative in relatives.iterrows():
-            assert aadr_samples[relative[0]] == aadr_samples[relative[1]]
+        for relationship in relatives.iterrows():
+            assert aadr_samples[relationship[0]] == aadr_samples[relationship[1]]

From f1eb9bba465cc0488c9ee3111c117d119f369e20 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <megametagross@outlook.de>
Date: Mon, 27 Jun 2022 15:50:55 +0300
Subject: [PATCH 22/56] [GRAPE-125] Added test data downloading, removed _get
 functions

---
 test/test.py | 96 +++++++++++++++++++++++++++++++++-------------------
 1 file changed, 61 insertions(+), 35 deletions(-)

diff --git a/test/test.py b/test/test.py
index d84b0318..58915a79 100644
--- a/test/test.py
+++ b/test/test.py
@@ -3,11 +3,16 @@
 import docker
 import csv
 import shutil
+import json
+import hashlib
 
 from datetime import datetime
 from reference_directory import ReferenceDirectory
 
 
+with open('../test_data.json') as config:
+    TEST_DATA_CONFIG = json.load(config)
+
 HOME_DIRECTORY = os.path.expanduser('~')
 
 GRAPE_DOCKERFILE = 'containers/snakemake/Dockerfile'
@@ -24,24 +29,22 @@
 AADR_SAMPLES_FILEPATH = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
 
 
-def _get_download_reference_command(reference_directory):
-    return f'launcher.py reference --use-bundle --ref-directory {reference_directory} ' \
-            '--phase --impute --real-run'
-
-
-def _get_simulate_command(reference_directory, working_directory, flow):
-    return f'launcher.py simulate --ref-directory {reference_directory} --cores 8 ' \
-           f'--directory {working_directory} --flow {flow} --assembly hg37 --seed 42 --real-run'
-
 
-def _get_preprocess_command(reference_directory, working_directory, input_file):
-    return f'launcher.py preprocess --ref-directory {reference_directory} --cores 8 ' \
-           f'--directory {working_directory} --vcf-file {input_file} --assembly hg37 --real-run'
+def _download_test_data(test_data_directory):
+    url = TEST_DATA_CONFIG['download']['url']
+    key = TEST_DATA_CONFIG['download']['azure_public_key']
+    file = TEST_DATA_CONFIG['download']['file']
+    md5_sum = TEST_DATA_CONFIG['download']['md5']
 
+    os.system(f'wget "{url}/{key}" -O {test_data_directory}/{file} --tries 50')
+    with open(os.path.join(test_data_directory, file), 'rb') as test_data_tar:
+        data = test_data_tar.read()
+        md5_returned = hashlib.md5(data).hexdigest()
+        if md5_returned != md5_sum:
+            return True
+        else:
+            return False
 
-def _get_find_command(reference_directory, working_directory):
-    return f'launcher.py find --ref-directory {reference_directory} --cores 8 ' \
-           f'--directory {working_directory} --flow ibis --real-run'
 
 
 def _read_metrics_file(filepath):
@@ -63,8 +66,8 @@ def _read_samples_file(filepath):
     with open(filepath, 'r') as samples_file:
         reader = csv.DictReader(samples_file)
         for row in reader:
-            sample_id = row['id']
-            samples[sample_id] = row['date']
+            sample = row['id']
+            samples[sample] = row['date']
 
     return samples
 
@@ -74,8 +77,8 @@ def _read_relatives_file(filepath):
     with open(filepath, 'r') as relatives_file:
         reader = csv.DictReader(relatives_file, delimiter="\t")
         for row in reader:
-            relationship = (row['id1'], row['id2'])
-            relatives.append(relationship)
+            relative = (row['id1'], row['id2'])
+            relatives.append(relative)
 
     return relatives
 
@@ -102,12 +105,37 @@ def grape_image(docker_client):
     docker_client.images.remove(GRAPE_IMAGE_TAG, force=True, noprune=False)
 
 
+@pytest.fixture
+def test_data_directory():
+    content = TEST_DATA_CONFIG['content']
+    actual_content = {}
+
+    if not os.path.exists(TESTING_REAL_DATA_DIRECTORY):
+        print('No test data found, new test data archive will be downloaded!')
+        if not _download_test_data(TESTING_REAL_DATA_DIRECTORY):
+            raise Exception('Test data archive download failed!')
+
+    for root, _, filenames in os.walk(TESTING_REAL_DATA_DIRECTORY):
+        for filename in filenames:
+            filepath = os.path.join(root, filename)
+            relative_path = os.path.relpath(filepath, reference_directory_path)
+            actual_content[relative_path] = os.path.getsize(filepath)
+
+    if actual_content != content:
+        print('Current test data files seem not match "test_data.json", new test data archive will be downloaded!')
+        if not _download_test_data(TESTING_REAL_DATA_DIRECTORY):
+            raise Exception('Test data archive download failed!')
+
+    return TESTING_REAL_DATA_DIRECTORY
+
+
 @pytest.fixture
 def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
     reference_directory = ReferenceDirectory(REFERENCE_DIRECTORY)
 
     if not reference_directory.is_valid():
-        command = _get_download_reference_command(CONTAINER_REFERENCE_DIRECTORY)
+        command = f'launcher.py reference --use-bundle --ref-directory {CONTAINER_REFERENCE_DIRECTORY} ' \
+            '--phase --impute --real-run'
         volumes = {
             reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'rw'}
         }
@@ -117,11 +145,6 @@ def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
     return reference_directory
 
 
-@pytest.fixture
-def test_data_directory():
-    return TESTING_REAL_DATA_DIRECTORY
-
-
 @pytest.fixture(scope="function")
 def working_directory(request):
     utc_timestamp = datetime.utcnow().strftime("%Y%m%d-%H%M%S-utc")
@@ -136,29 +159,32 @@ def working_directory(request):
 
 @pytest.fixture(scope="function")
 def simulate_command(request):
-    return _get_simulate_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY, request.param);
+    return f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+           f'--directory {CONTAINER_WORKING_DIRECTORY} --flow {request.param} --assembly hg37 --seed 42 --real-run';
 
 
 @pytest.fixture()
 def find_command():
-    return _get_find_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY);
+    return f'launcher.py find --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+           f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --real-run';
 
 
 @pytest.fixture(scope="function")
 def preprocess_command(request):
-    return _get_preprocess_command(CONTAINER_REFERENCE_DIRECTORY, CONTAINER_WORKING_DIRECTORY, request.param);
+    return f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+           f'--directory {CONTAINER_WORKING_DIRECTORY} --vcf-file {request.param} --assembly hg37 --real-run';
 
 
-simulation_list = [('ibis', 'simulation-ibis'),
-                   ('ibis-king', 'simulation-ibis-king'),
+simulation_list = [('ibis', 'simulation-ibis', 'ibis'),
+                   ('ibis-king', 'simulation-ibis-king', 'ibis-king'),
                    ('germline-king --assembly hg38 --phase --impute',  # germline needs extra flags to work
-                    'simulation-germline-king')]
+                    'simulation-germline-king', 'germline-king')]
 
-real_data_list = [('realdata-khazar', KHAZAR_VCF),
-                  ('realdata-aadr', f'{AADR_VCF} --het-samples 0.0')]  # ancient samples have zero heterozygosity
+real_data_list = [('real-khazar', KHAZAR_VCF, 'khazar'),
+                  ('real-aadr', f'{AADR_VCF} --het-samples 0.0', 'aadr')]  # ancient samples have zero heterozygosity
 
 
-@pytest.mark.parametrize('simulate_command,working_directory', simulation_list, indirect=True)
+@pytest.mark.parametrize('simulate_command,working_directory,test_name', simulation_list, indirect=True)
 def test_simulation(docker_client, grape_image, reference_directory, working_directory, simulate_command):
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
@@ -184,7 +210,7 @@ def test_simulation(docker_client, grape_image, reference_directory, working_dir
     assert metrics['9']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
 
 
-@pytest.mark.parametrize('working_directory,preprocess_command', real_data_list, indirect=True)
+@pytest.mark.parametrize('working_directory,preprocess_command,test_name', real_data_list, indirect=True)
 def test_real_data(docker_client, grape_image, reference_directory,
                    working_directory, test_data_directory, find_command, preprocess_command):
     volumes = {

From 9d10b6f98f2f6f1d508f382e12b89d42f842b8cc Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <megametagross@outlook.de>
Date: Mon, 27 Jun 2022 15:52:16 +0300
Subject: [PATCH 23/56] [GRAPE-125] Info needed for test data downloading

---
 test/test_data.json | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 test/test_data.json

diff --git a/test/test_data.json b/test/test_data.json
new file mode 100644
index 00000000..61c94797
--- /dev/null
+++ b/test/test_data.json
@@ -0,0 +1,14 @@
+{
+   "download": {
+      "file": "test_data.tar.gz",
+      "url": "https://bioinformatics.file.core.windows.net/test/test_data.tar.gz",
+      "filesize": 3462612,
+      "md5": "c497d0e9840d847c9d8d1b050b4e2427",
+      "azure_public_key": "?sv=2020-08-04&ss=f&srt=sco&sp=r&se=2022-08-08T14:35:53Z&st=2021-08-27T06:35:53Z&spr=https&sig=SjxrSn2KBuQYjYgT2ZZTHQ6IOhA%2BRUSvLIgog%2FH2Tnk%3D"
+   },
+   "content": {
+      "aadr.reheaded.vcf.gz": 3556010338,
+      "aadr_samples.csv": 283133,
+      "khazar314.vcf.gz": 31235749
+   }
+}

From b6a77cf6e975b01c0762226d794de33c393a466e Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Thu, 30 Jun 2022 14:29:47 +0000
Subject: [PATCH 24/56] [GRAPE-125] Made separate test from test_simulate and
 test_real_data

---
 test/test.py | 148 ++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 106 insertions(+), 42 deletions(-)

diff --git a/test/test.py b/test/test.py
index 58915a79..e2dbfa56 100644
--- a/test/test.py
+++ b/test/test.py
@@ -9,16 +9,16 @@
 from datetime import datetime
 from reference_directory import ReferenceDirectory
 
-
-with open('../test_data.json') as config:
+dirname = os.path.dirname(__file__)
+with open(os.path.join(dirname, 'test_data.json')) as config:
     TEST_DATA_CONFIG = json.load(config)
 
-HOME_DIRECTORY = os.path.expanduser('~')
+HOME_DIRECTORY = os.path.expanduser('/media')
 
 GRAPE_DOCKERFILE = 'containers/snakemake/Dockerfile'
 GRAPE_IMAGE_TAG = 'genx_relatives:latest'
 
-REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref')
+REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref_test')
 CONTAINER_REFERENCE_DIRECTORY = '/media/ref'
 CONTAINER_WORKING_DIRECTORY = '/media/data'
 TESTING_REAL_DATA_DIRECTORY = '/media/test_data'
@@ -29,7 +29,6 @@
 AADR_SAMPLES_FILEPATH = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
 
 
-
 def _download_test_data(test_data_directory):
     url = TEST_DATA_CONFIG['download']['url']
     key = TEST_DATA_CONFIG['download']['azure_public_key']
@@ -46,7 +45,6 @@ def _download_test_data(test_data_directory):
             return False
 
 
-
 def _read_metrics_file(filepath):
     metrics = {}
     with open(filepath, 'r') as metrics_file:
@@ -98,11 +96,12 @@ def grape_image(docker_client):
         path='.', dockerfile=GRAPE_DOCKERFILE, tag=GRAPE_IMAGE_TAG,
         rm=True, container_limits={'memory': 8 * 1024 * 1024 * 1024}
     )
-
+    print(f'\nCreated docker image with tag {GRAPE_IMAGE_TAG}')
     yield docker_client.images.get(GRAPE_IMAGE_TAG)
 
     # Fixture teardown to remove GRAPE Docker image
     docker_client.images.remove(GRAPE_IMAGE_TAG, force=True, noprune=False)
+    print(f'\nRemoved docker image with tag {GRAPE_IMAGE_TAG}')
 
 
 @pytest.fixture
@@ -111,18 +110,18 @@ def test_data_directory():
     actual_content = {}
 
     if not os.path.exists(TESTING_REAL_DATA_DIRECTORY):
-        print('No test data found, new test data archive will be downloaded!')
+        print('\nNo test data found, new test data archive will be downloaded!')
         if not _download_test_data(TESTING_REAL_DATA_DIRECTORY):
             raise Exception('Test data archive download failed!')
 
     for root, _, filenames in os.walk(TESTING_REAL_DATA_DIRECTORY):
         for filename in filenames:
             filepath = os.path.join(root, filename)
-            relative_path = os.path.relpath(filepath, reference_directory_path)
+            relative_path = os.path.relpath(filepath, TESTING_REAL_DATA_DIRECTORY)
             actual_content[relative_path] = os.path.getsize(filepath)
 
     if actual_content != content:
-        print('Current test data files seem not match "test_data.json", new test data archive will be downloaded!')
+        print('\nCurrent test data files seem not match "test_data.json", new test data archive will be downloaded!')
         if not _download_test_data(TESTING_REAL_DATA_DIRECTORY):
             raise Exception('Test data archive download failed!')
 
@@ -134,6 +133,8 @@ def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
     reference_directory = ReferenceDirectory(REFERENCE_DIRECTORY)
 
     if not reference_directory.is_valid():
+        print('\nCurrrent reference data files seem not match '
+              '"reference_directory_content.json", new reference data archive will be downloaded!')
         command = f'launcher.py reference --use-bundle --ref-directory {CONTAINER_REFERENCE_DIRECTORY} ' \
             '--phase --impute --real-run'
         volumes = {
@@ -157,40 +158,46 @@ def working_directory(request):
     shutil.rmtree(working_directory_path)
 
 
-@pytest.fixture(scope="function")
-def simulate_command(request):
-    return f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
-           f'--directory {CONTAINER_WORKING_DIRECTORY} --flow {request.param} --assembly hg37 --seed 42 --real-run';
-
+@pytest.mark.parametrize('working_directory', ['ibis'], indirect=True)
+def test_simulation_ibis(docker_client, grape_image, reference_directory, working_directory):
+    volumes = {
+        reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
+        working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'}
+    }
 
-@pytest.fixture()
-def find_command():
-    return f'launcher.py find --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
-           f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --real-run';
+    simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 '\
+                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --assembly hg37 --seed 42 --real-run'
 
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
 
-@pytest.fixture(scope="function")
-def preprocess_command(request):
-    return f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
-           f'--directory {CONTAINER_WORKING_DIRECTORY} --vcf-file {request.param} --assembly hg37 --real-run';
+    # Read file result with simulation metrics
+    metrics = _read_metrics_file(os.path.join(working_directory, METRICS_FILEPATH))
 
+    # Validate simultation metrics
+    assert metrics['1']['Recall'] > 0.99 and metrics['1']['Precision'] > 0.99
+    assert metrics['2']['Recall'] > 0.99 and metrics['2']['Precision'] > 0.99
+    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.99
 
-simulation_list = [('ibis', 'simulation-ibis', 'ibis'),
-                   ('ibis-king', 'simulation-ibis-king', 'ibis-king'),
-                   ('germline-king --assembly hg38 --phase --impute',  # germline needs extra flags to work
-                    'simulation-germline-king', 'germline-king')]
+    assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
+    assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95
+    assert metrics['6']['Recall'] > 0.80 and metrics['6']['Precision'] > 0.90
 
-real_data_list = [('real-khazar', KHAZAR_VCF, 'khazar'),
-                  ('real-aadr', f'{AADR_VCF} --het-samples 0.0', 'aadr')]  # ancient samples have zero heterozygosity
+    assert metrics['7']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+    assert metrics['8']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+    assert metrics['9']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
 
 
-@pytest.mark.parametrize('simulate_command,working_directory,test_name', simulation_list, indirect=True)
-def test_simulation(docker_client, grape_image, reference_directory, working_directory, simulate_command):
+@pytest.mark.parametrize('working_directory', ['ibis-king'], indirect=True)
+def test_simulation_king(docker_client, grape_image, reference_directory, working_directory):
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
         working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'}
     }
 
+    simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis-king --assembly hg37 ' \
+                       f'--seed 42 --real-run'
+
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
 
     # Read file result with simulation metrics
@@ -210,15 +217,77 @@ def test_simulation(docker_client, grape_image, reference_directory, working_dir
     assert metrics['9']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
 
 
-@pytest.mark.parametrize('working_directory,preprocess_command,test_name', real_data_list, indirect=True)
-def test_real_data(docker_client, grape_image, reference_directory,
-                   working_directory, test_data_directory, find_command, preprocess_command):
+@pytest.mark.parametrize('working_directory', ['germline-king'], indirect=True)
+def test_simulation_germline_king(docker_client, grape_image, reference_directory, working_directory):
+    volumes = {
+        reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
+        working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'}
+    }
+
+    simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow germline-king --assembly hg38 ' \
+                       f'--phase --impute --seed 42 --real-run'
+
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
+
+    # Read file result with simulation metrics
+    metrics = _read_metrics_file(os.path.join(working_directory, METRICS_FILEPATH))
+
+    # Validate simultation metrics
+    assert metrics['1']['Recall'] > 0.99 and metrics['1']['Precision'] > 0.99
+    assert metrics['2']['Recall'] > 0.99 and metrics['2']['Precision'] > 0.99
+    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.99
+
+    assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
+    assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95
+    assert metrics['6']['Recall'] > 0.80 and metrics['6']['Precision'] > 0.90
+
+    assert metrics['7']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+    assert metrics['8']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+    assert metrics['9']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
+
+
+@pytest.mark.parametrize('working_directory', ['khazar'], indirect=True)
+def test_khazar(docker_client, grape_image, reference_directory, working_directory, test_data_directory):
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
         working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'},
         test_data_directory: {'bind': TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
     }
 
+    preprocess_command = f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+                         f'--directory {CONTAINER_WORKING_DIRECTORY} --vcf-file {KHAZAR_VCF} ' \
+                         f'--assembly hg37 --real-run'
+
+    find_command = f'launcher.py find --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+                   f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --real-run'
+
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=preprocess_command, volumes=volumes)
+    docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=find_command, volumes=volumes)
+
+    # Read file result with relatives
+    relatives = _read_relatives_file(os.path.join(working_directory, RELATIVES_FILEPATH))
+
+    # Validate relatives
+    num_of_relatives = len(list(relatives))
+    assert 55 >= num_of_relatives >= 57
+
+
+@pytest.mark.parametrize('working_directory', ['aadr'], indirect=True)
+def test_aadr(docker_client, grape_image, reference_directory, working_directory, test_data_directory):
+    volumes = {
+        reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
+        working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'},
+        test_data_directory: {'bind': TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
+    }
+
+    preprocess_command = f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+                         f'--directory {CONTAINER_WORKING_DIRECTORY} --vcf-file {KHAZAR_VCF} --het-samples 0.0 ' \
+                         f'--assembly hg37 --real-run'
+
+    find_command = f'launcher.py find --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
+                   f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --real-run'
+
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=preprocess_command, volumes=volumes)
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=find_command, volumes=volumes)
 
@@ -226,11 +295,6 @@ def test_real_data(docker_client, grape_image, reference_directory,
     relatives = _read_relatives_file(os.path.join(working_directory, RELATIVES_FILEPATH))
 
     # Validate relatives
-    current_data = working_directory.split('-')[0]
-    if current_data == 'khazar':
-        num_of_relatives = len(list(relatives))
-        assert 55 >= num_of_relatives >= 57
-    elif current_data == 'aadr':
-        aadr_samples = _read_samples_file(AADR_SAMPLES_FILEPATH)
-        for relationship in relatives.iterrows():
-            assert aadr_samples[relationship[0]] == aadr_samples[relationship[1]]
+    aadr_samples = _read_samples_file(AADR_SAMPLES_FILEPATH)
+    for relationship in relatives.iterrows():
+        assert aadr_samples[relationship[0]] == aadr_samples[relationship[1]]
\ No newline at end of file

From 1a33442d2b4d0b74986fdd97f3a474f8ca704a28 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Thu, 30 Jun 2022 16:20:19 +0000
Subject: [PATCH 25/56] [GRAPE-125] Fixed minor issues

---
 test/test.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test.py b/test/test.py
index e2dbfa56..e0191830 100644
--- a/test/test.py
+++ b/test/test.py
@@ -270,7 +270,7 @@ def test_khazar(docker_client, grape_image, reference_directory, working_directo
 
     # Validate relatives
     num_of_relatives = len(list(relatives))
-    assert 55 >= num_of_relatives >= 57
+    assert 56 <= num_of_relatives >= 58
 
 
 @pytest.mark.parametrize('working_directory', ['aadr'], indirect=True)
@@ -296,5 +296,5 @@ def test_aadr(docker_client, grape_image, reference_directory, working_directory
 
     # Validate relatives
     aadr_samples = _read_samples_file(AADR_SAMPLES_FILEPATH)
-    for relationship in relatives.iterrows():
+    for relationship in relatives:
         assert aadr_samples[relationship[0]] == aadr_samples[relationship[1]]
\ No newline at end of file

From 0a9593952268fef26302773bac5e07d1997206a8 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Mon, 11 Jul 2022 07:15:05 +0000
Subject: [PATCH 26/56] [GRAPE-125] Adjusted preprocess params and metrics
 assertion

---
 test/test.py | 44 +++++++++++++++++++++++++++-----------------
 1 file changed, 27 insertions(+), 17 deletions(-)

diff --git a/test/test.py b/test/test.py
index e0191830..ea837676 100644
--- a/test/test.py
+++ b/test/test.py
@@ -2,9 +2,9 @@
 import pytest
 import docker
 import csv
-import shutil
 import json
 import hashlib
+import tarfile
 
 from datetime import datetime
 from reference_directory import ReferenceDirectory
@@ -34,15 +34,21 @@ def _download_test_data(test_data_directory):
     key = TEST_DATA_CONFIG['download']['azure_public_key']
     file = TEST_DATA_CONFIG['download']['file']
     md5_sum = TEST_DATA_CONFIG['download']['md5']
+    tar = os.path.join(test_data_directory, file)
 
-    os.system(f'wget "{url}/{key}" -O {test_data_directory}/{file} --tries 50')
-    with open(os.path.join(test_data_directory, file), 'rb') as test_data_tar:
+    os.system(f'wget "{url}{key}" -O {tar} --tries 50')
+
+    with open(tar, 'rb') as test_data_tar:
         data = test_data_tar.read()
         md5_returned = hashlib.md5(data).hexdigest()
-        if md5_returned != md5_sum:
-            return True
-        else:
-            return False
+    if md5_returned == md5_sum:
+        test_tar = tarfile.open(tar)
+        test_tar.extractall(test_data_directory)
+        test_tar.close()
+        os.remove(tar)
+        return True
+    else:
+        return False
 
 
 def _read_metrics_file(filepath):
@@ -110,6 +116,7 @@ def test_data_directory():
     actual_content = {}
 
     if not os.path.exists(TESTING_REAL_DATA_DIRECTORY):
+        os.makedirs(TESTING_REAL_DATA_DIRECTORY)
         print('\nNo test data found, new test data archive will be downloaded!')
         if not _download_test_data(TESTING_REAL_DATA_DIRECTORY):
             raise Exception('Test data archive download failed!')
@@ -155,7 +162,7 @@ def working_directory(request):
     yield working_directory_path
 
     # Fixture teardown to remove working directory
-    shutil.rmtree(working_directory_path)
+    #shutil.rmtree(working_directory_path)
 
 
 @pytest.mark.parametrize('working_directory', ['ibis'], indirect=True)
@@ -166,7 +173,7 @@ def test_simulation_ibis(docker_client, grape_image, reference_directory, workin
     }
 
     simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 '\
-                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --assembly hg37 --seed 42 --real-run'
+                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis --assembly hg37 --seed 42 --real-run' \
 
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
 
@@ -196,7 +203,7 @@ def test_simulation_king(docker_client, grape_image, reference_directory, workin
 
     simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
                        f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis-king --assembly hg37 ' \
-                       f'--seed 42 --real-run'
+                       f'--sim-params-file params/relatives_big.def --sim-samples-file all.tsv --seed 42 --real-run'
 
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
 
@@ -225,8 +232,8 @@ def test_simulation_germline_king(docker_client, grape_image, reference_director
     }
 
     simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
-                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow germline-king --assembly hg38 ' \
-                       f'--phase --impute --seed 42 --real-run'
+                       f'--directory {CONTAINER_WORKING_DIRECTORY} --flow germline-king ' \
+                       f'--phase --impute --assembly hg37 --real-run --seed 42 '
 
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
 
@@ -236,11 +243,11 @@ def test_simulation_germline_king(docker_client, grape_image, reference_director
     # Validate simultation metrics
     assert metrics['1']['Recall'] > 0.99 and metrics['1']['Precision'] > 0.99
     assert metrics['2']['Recall'] > 0.99 and metrics['2']['Precision'] > 0.99
-    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.99
+    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.98
 
     assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
     assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95
-    assert metrics['6']['Recall'] > 0.80 and metrics['6']['Precision'] > 0.90
+    assert metrics['6']['Recall'] > 0.79 and metrics['6']['Precision'] > 0.90
 
     assert metrics['7']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
     assert metrics['8']['Recall'] > 0 and metrics['1']['Precision'] > 0.9
@@ -270,7 +277,7 @@ def test_khazar(docker_client, grape_image, reference_directory, working_directo
 
     # Validate relatives
     num_of_relatives = len(list(relatives))
-    assert 56 <= num_of_relatives >= 58
+    assert 55 <= num_of_relatives <= 57
 
 
 @pytest.mark.parametrize('working_directory', ['aadr'], indirect=True)
@@ -282,7 +289,7 @@ def test_aadr(docker_client, grape_image, reference_directory, working_directory
     }
 
     preprocess_command = f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
-                         f'--directory {CONTAINER_WORKING_DIRECTORY} --vcf-file {KHAZAR_VCF} --het-samples 0.0 ' \
+                         f'--directory {CONTAINER_WORKING_DIRECTORY} --vcf-file {AADR_VCF} --het-samples 0.0 ' \
                          f'--assembly hg37 --real-run'
 
     find_command = f'launcher.py find --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
@@ -296,5 +303,8 @@ def test_aadr(docker_client, grape_image, reference_directory, working_directory
 
     # Validate relatives
     aadr_samples = _read_samples_file(AADR_SAMPLES_FILEPATH)
+    failed_relations = 0
     for relationship in relatives:
-        assert aadr_samples[relationship[0]] == aadr_samples[relationship[1]]
\ No newline at end of file
+        if aadr_samples[relationship[0]] != aadr_samples[relationship[1]]:
+            failed_relations += 1
+    assert failed_relations < 2
\ No newline at end of file

From 590b61e09040180df45779cbd2f3437497d11425 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Mon, 11 Jul 2022 07:16:28 +0000
Subject: [PATCH 27/56] [GRAPE-125] Changed the link to download from bundle
 folder

---
 test/test_data.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/test_data.json b/test/test_data.json
index 61c94797..bc45fbad 100644
--- a/test/test_data.json
+++ b/test/test_data.json
@@ -1,7 +1,7 @@
 {
    "download": {
       "file": "test_data.tar.gz",
-      "url": "https://bioinformatics.file.core.windows.net/test/test_data.tar.gz",
+      "url": "https://bioinformatics.file.core.windows.net/bundles/test_data.tar.gz",
       "filesize": 3462612,
       "md5": "c497d0e9840d847c9d8d1b050b4e2427",
       "azure_public_key": "?sv=2020-08-04&ss=f&srt=sco&sp=r&se=2022-08-08T14:35:53Z&st=2021-08-27T06:35:53Z&spr=https&sig=SjxrSn2KBuQYjYgT2ZZTHQ6IOhA%2BRUSvLIgog%2FH2Tnk%3D"

From cb7889ca76e8c7865cd8dc2cb4ae70d4e31a8dd7 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Mon, 11 Jul 2022 10:19:27 +0300
Subject: [PATCH 28/56] [GRAPE-125] Changed test trigger

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4dc0347d..aa73c599 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -2,7 +2,7 @@ name: Run Python Tests
 
 on:
   pull_request:
-    branches: [ master ]
+    branches: [ develop ]
     types: [ opened ]
 
   workflow_dispatch:

From 51278d7ae704d721eb04d349e35a945fcae36141 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Tue, 12 Jul 2022 08:51:27 +0000
Subject: [PATCH 29/56] [GRAPE-125] Testing pytest

---
 .github/workflows/pytest.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index aa73c599..8bacfdea 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -2,18 +2,20 @@ name: Run Python Tests
 
 on:
   pull_request:
-    branches: [ develop ]
+    branches: [ master ]
     types: [ opened ]
 
   workflow_dispatch:
 
+  push:
+
 jobs:
   test:
     # Self-hosted runner
     runs-on: self-hosted
-    if: |
-      !github.event.pull_request.head.repo.fork &&
-      github.head_ref == 'develop'
+    # if: |
+    #   !github.event.pull_request.head.repo.fork &&
+    #   github.head_ref == 'develop'
 
     steps:
       - uses: actions/checkout@v3
@@ -24,4 +26,4 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r test/requirements.txt
       - run: |
-          pytest test/test.py
+          pytest test/test.py
\ No newline at end of file

From ebdd1e2b36b83b6e5221df1ec789a8b2b1af471c Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Tue, 12 Jul 2022 14:54:25 +0000
Subject: [PATCH 30/56] [GRAPE-125] Added container dir for test data

---
 test/test.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/test.py b/test/test.py
index ea837676..7d39460e 100644
--- a/test/test.py
+++ b/test/test.py
@@ -21,7 +21,8 @@
 REFERENCE_DIRECTORY = os.path.join(HOME_DIRECTORY, 'ref_test')
 CONTAINER_REFERENCE_DIRECTORY = '/media/ref'
 CONTAINER_WORKING_DIRECTORY = '/media/data'
-TESTING_REAL_DATA_DIRECTORY = '/media/test_data'
+TESTING_REAL_DATA_DIRECTORY = os.path.join(HOME_DIRECTORY, 'test_data')
+CONTAINER_TESTING_REAL_DATA_DIRECTORY = '/media/test_data'
 KHAZAR_VCF = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'khazar314.vcf.gz')
 AADR_VCF = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr.reheaded.vcf.gz')
 METRICS_FILEPATH = 'results/metrics.tsv'
@@ -259,7 +260,7 @@ def test_khazar(docker_client, grape_image, reference_directory, working_directo
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
         working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'},
-        test_data_directory: {'bind': TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
+        test_data_directory: {'bind': CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
     }
 
     preprocess_command = f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
@@ -285,7 +286,7 @@ def test_aadr(docker_client, grape_image, reference_directory, working_directory
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
         working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'},
-        test_data_directory: {'bind': TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
+        test_data_directory: {'bind': CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'mode': 'ro'}
     }
 
     preprocess_command = f'launcher.py preprocess --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \

From e6dd4003fd6862e793258d1a8f84fb8264eef7d3 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Tue, 12 Jul 2022 14:56:09 +0000
Subject: [PATCH 31/56] [GRAPE-125] Adjusted ibis-king simulation metrics

---
 test/test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/test.py b/test/test.py
index 7d39460e..45251df6 100644
--- a/test/test.py
+++ b/test/test.py
@@ -214,7 +214,7 @@ def test_simulation_king(docker_client, grape_image, reference_directory, workin
     # Validate simultation metrics
     assert metrics['1']['Recall'] > 0.99 and metrics['1']['Precision'] > 0.99
     assert metrics['2']['Recall'] > 0.99 and metrics['2']['Precision'] > 0.99
-    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.98
+    assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.97
 
     assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
     assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95

From f42ffe2e118d95f7c51c1d193e780e7af97b5e2a Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Tue, 12 Jul 2022 20:26:52 +0000
Subject: [PATCH 32/56] [GRAPE-125] Changed home directory

---
 test/test.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test.py b/test/test.py
index 45251df6..24526466 100644
--- a/test/test.py
+++ b/test/test.py
@@ -13,7 +13,7 @@
 with open(os.path.join(dirname, 'test_data.json')) as config:
     TEST_DATA_CONFIG = json.load(config)
 
-HOME_DIRECTORY = os.path.expanduser('/media')
+HOME_DIRECTORY = os.path.expanduser('~')
 
 GRAPE_DOCKERFILE = 'containers/snakemake/Dockerfile'
 GRAPE_IMAGE_TAG = 'genx_relatives:latest'
@@ -217,7 +217,7 @@ def test_simulation_king(docker_client, grape_image, reference_directory, workin
     assert metrics['3']['Recall'] > 0.99 and metrics['3']['Precision'] > 0.97
 
     assert metrics['4']['Recall'] > 0.90 and metrics['4']['Precision'] > 0.95
-    assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.95
+    assert metrics['5']['Recall'] > 0.90 and metrics['5']['Precision'] > 0.94
     assert metrics['6']['Recall'] > 0.80 and metrics['6']['Precision'] > 0.90
 
     assert metrics['7']['Recall'] > 0 and metrics['1']['Precision'] > 0.9

From dafebc28d6542ff5e6612bb39cbbe99cfe32e84d Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Wed, 13 Jul 2022 07:33:23 +0000
Subject: [PATCH 33/56] [GRAPE-125] Small fixes

---
 test/test.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/test.py b/test/test.py
index 24526466..7d8ff3c9 100644
--- a/test/test.py
+++ b/test/test.py
@@ -23,11 +23,11 @@
 CONTAINER_WORKING_DIRECTORY = '/media/data'
 TESTING_REAL_DATA_DIRECTORY = os.path.join(HOME_DIRECTORY, 'test_data')
 CONTAINER_TESTING_REAL_DATA_DIRECTORY = '/media/test_data'
-KHAZAR_VCF = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'khazar314.vcf.gz')
-AADR_VCF = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr.reheaded.vcf.gz')
+KHAZAR_VCF = os.path.join(CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'khazar314.vcf.gz')
+AADR_VCF = os.path.join(CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'aadr.reheaded.vcf.gz')
 METRICS_FILEPATH = 'results/metrics.tsv'
 RELATIVES_FILEPATH = 'results/relatives.tsv'
-AADR_SAMPLES_FILEPATH = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
+AADR_SAMPLES_FILEPATH = os.path.join(CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
 
 
 def _download_test_data(test_data_directory):
@@ -204,7 +204,7 @@ def test_simulation_king(docker_client, grape_image, reference_directory, workin
 
     simulate_command = f'launcher.py simulate --ref-directory {CONTAINER_REFERENCE_DIRECTORY} --cores 8 ' \
                        f'--directory {CONTAINER_WORKING_DIRECTORY} --flow ibis-king --assembly hg37 ' \
-                       f'--sim-params-file params/relatives_big.def --sim-samples-file all.tsv --seed 42 --real-run'
+                       f'--seed 42 --real-run'
 
     docker_client.containers.run(GRAPE_IMAGE_TAG, remove=True, command=simulate_command, volumes=volumes)
 

From 7dd4dc817ca89a89701a94d79254c279bba9cbb3 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <megametagross@outlook.de>
Date: Wed, 13 Jul 2022 11:51:58 +0300
Subject: [PATCH 34/56] [GRAPE-128] Precreation of conda envs

---
 containers/snakemake/Dockerfile      |  4 ++--
 rules/filter.smk                     | 10 +++++-----
 rules/imputation.smk                 |  8 ++++----
 rules/phasing.smk                    |  2 +-
 rules/preprocessing.smk              | 22 +++++++++++-----------
 rules/relatives.smk                  | 16 ++++++++--------
 rules/relatives_ibis.smk             | 10 +++++-----
 rules/relatives_ibis_king.smk        | 14 +++++++-------
 workflows/bundle/Snakefile           |  4 ++--
 workflows/pedsim/Snakefile           | 10 +++++-----
 workflows/preprocess_vcf/Snakefile   |  4 ++--
 workflows/reference/Snakefile        | 24 ++++++++++++------------
 workflows/remove_relatives/Snakefile |  8 ++++----
 workflows/simbig/Snakefile           | 14 +++++++-------
 workflows/weight/Snakefile           |  4 ++--
 15 files changed, 77 insertions(+), 77 deletions(-)

diff --git a/containers/snakemake/Dockerfile b/containers/snakemake/Dockerfile
index bd575212..83923b55 100644
--- a/containers/snakemake/Dockerfile
+++ b/containers/snakemake/Dockerfile
@@ -5,7 +5,7 @@ ENV DEBIAN_FRONTEND noninteractive
 RUN apt-get clean && apt-get update && apt-get install -y ca-certificates libseccomp-dev squashfs-tools \
     && rm -rf /tmp/*
 
-ADD envs/snakemake.yaml envs/snakemake.yaml
+ADD envs envs
 
 ENV PATH /opt/conda/bin:${PATH}
 ENV LANG C.UTF-8
@@ -16,7 +16,7 @@ RUN apt-get install -y wget bzip2 gnupg2 git libgomp1 && \
     bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniconda3-latest-Linux-x86_64.sh && \
     conda install -c conda-forge mamba && \
-    mamba env create -f envs/snakemake.yaml && \
+    for e in envs/*; do mamba env create -f $e ; done && \
     conda clean --all -y
 
 # Intall Minimac3
diff --git a/rules/filter.smk b/rules/filter.smk
index e6df4cd7..f97c9f01 100644
--- a/rules/filter.smk
+++ b/rules/filter.smk
@@ -7,7 +7,7 @@ rule vcf_stats:
     params:
         samples='vcf/{batch}_merged_lifted.vcf.samples'
     conda:
-        '../envs/bcftools.yaml'
+        'bcftools'
     shell:
         """
             bcftools query --list-samples {input.vcf} > {params.samples}
@@ -29,7 +29,7 @@ rule select_bad_samples:
         alt_hom_samples = config['alt_hom_samples'],
         het_samples = config['het_samples']
     conda:
-        '../envs/evaluation.yaml'
+        'evaluation'
     script:
         '../scripts/select_bad_samples.py'
 
@@ -43,7 +43,7 @@ rule plink_filter:
         bim = temp('plink/{batch}_merged_filter.bim'),
         fam = temp('plink/{batch}_merged_filter.fam')
     conda:
-        '../envs/plink.yaml'
+        'plink'
     params:
         input   = '{batch}_merged',
         out     = '{batch}_merged_filter',
@@ -90,7 +90,7 @@ rule plink_clean_up:
         input = 'plink/{batch}_merged_filter',
         out = 'plink/{batch}_merged_mapped'
     conda:
-        '../envs/plink.yaml'
+        'plink'
     log:
         'logs/plink/{batch}_plink_clean_up.log'
     benchmark:
@@ -128,7 +128,7 @@ rule prepare_vcf:
         input   = 'plink/{batch}_merged_mapped',
         vcf     = 'vcf/{batch}_merged_mapped_sorted.vcf.gz'
     conda:
-         '../envs/bcf_plink.yaml'
+         'bcf_plink'
     log:
         plink='logs/plink/{batch}_prepare_vcf.log',
         vcf='logs/vcf/{batch}_prepare_vcf.log'
diff --git a/rules/imputation.smk b/rules/imputation.smk
index d13187d7..88324e89 100644
--- a/rules/imputation.smk
+++ b/rules/imputation.smk
@@ -29,7 +29,7 @@ rule imputation_filter:
     # TODO: because "The option is currently used only for the compression of the output stream"
     # threads: workflow.cores
     conda:
-        '../envs/bcftools.yaml'
+        'bcftools'
     log:
         'logs/impute/{batch}_imputation_filter-{chrom}.log'
     benchmark:
@@ -63,7 +63,7 @@ rule merge_imputation_filter:
         mode=config['mode'],
         merged_imputed = 'background/' + card + '_merged_imputed.vcf.gz'
     conda:
-        '../envs/bcftools.yaml'
+        'bcftools'
     log:
         'logs/vcf/' + card + '_merge_imputation_filter.log'
     benchmark:
@@ -103,7 +103,7 @@ rule convert_imputed_to_plink:
     params:
         out = 'plink/{batch}_merged_imputed'
     conda:
-        '../envs/plink.yaml'
+        'plink'
     log:
         'logs/plink/{batch}_convert_imputed_to_plink.log'
     benchmark:
@@ -126,7 +126,7 @@ rule merge_convert_imputed_to_plink:
         background  = 'background/{batch}_merged_imputed',
         out         = 'plink/client/{batch}_merged_imputed'
     conda:
-        '../envs/plink.yaml'
+        'plink'
     log:
         'logs/plink/{batch}_convert_imputed_to_plink.log'
     benchmark:
diff --git a/rules/phasing.smk b/rules/phasing.smk
index 6d68beba..184eeca3 100644
--- a/rules/phasing.smk
+++ b/rules/phasing.smk
@@ -31,7 +31,7 @@ rule merge_phased:
         list='vcf/{batch}_phased.merge.list',
         mode=config['mode']
     conda:
-        '../envs/bcftools.yaml'
+        'bcftools'
     log:
         'logs/vcf/{batch}_merged_phased.log'
     benchmark:
diff --git a/rules/preprocessing.smk b/rules/preprocessing.smk
index d258d586..aae06673 100644
--- a/rules/preprocessing.smk
+++ b/rules/preprocessing.smk
@@ -15,7 +15,7 @@ if NUM_BATCHES > 1:
         params:
             num_batches=NUM_BATCHES
         conda:
-            '../envs/bcftools.yaml'
+            'bcftools'
         shell:
             '''
             bcftools query --list-samples input.vcf.gz >> vcf/samples.txt
@@ -38,7 +38,7 @@ if NUM_BATCHES > 1:
         output:
             vcf='vcf/{batch}.vcf.gz'
         conda:
-            '../envs/bcftools.yaml'
+            'bcftools'
         shell:
             '''
             bcftools view -S {input.samples} {input.vcf} -O z -o {output.vcf} --force-samples
@@ -81,7 +81,7 @@ rule recode_vcf:
     output:
         vcf=temp('vcf/{batch}_merged_recoded.vcf.gz')
     conda:
-        '../envs/bcftools.yaml'
+        'bcftools'
     shell:
         '''
         rm -f chr_name_conv.txt
@@ -100,7 +100,7 @@ if assembly == 'hg38':
         output:
             vcf=temp('vcf/{batch}_merged_lifted.vcf.gz')
         conda:
-            '../envs/liftover.yaml'
+            'liftover'
         log:
             'logs/liftover/liftover{batch}.log'
         params:
@@ -129,7 +129,7 @@ rule recode_snp_ids:
     output:
         vcf=temp('vcf/{batch}_merged_lifted_id.vcf.gz')
     conda:
-        '../envs/bcftools.yaml'
+        'bcftools'
     shell:
         '''
             bcftools annotate --set-id "%CHROM:%POS:%REF:%FIRST_ALT" {input.vcf} -O z -o {output.vcf}
@@ -184,7 +184,7 @@ if NUM_BATCHES > 1:
         params:
             out='preprocessed/{batch}_data'
         conda:
-            '../envs/plink.yaml'
+            'plink'
         log:
             'logs/plink/convert_mapped_to_plink{batch}.log'
         benchmark:
@@ -215,7 +215,7 @@ if NUM_BATCHES > 1:
         threads:
             workflow.cores
         conda:
-            '../envs/plink.yaml'
+            'plink'
         shell:
             '''
             rm files_list.txt || true
@@ -238,7 +238,7 @@ if NUM_BATCHES > 1:
         output:
             batches_vcf_index=temp('preprocessed/{batch}_data.vcf.gz.csi')
         conda:
-            '../envs/bcftools.yaml'
+            'bcftools'
         shell:
             '''
             bcftools index -f {input.batches_vcf}
@@ -264,7 +264,7 @@ if NUM_BATCHES > 1:
             batches_vcf=expand('batch{s}_data.vcf.gz',s=BATCHES),
             vcf='data.vcf.gz'
         conda:
-            '../envs/bcftools.yaml'
+            'bcftools'
         shell:
             '''
             rm complete_vcf_list.txt || true
@@ -290,7 +290,7 @@ else:
         params:
             out='preprocessed/data'
         conda:
-            '../envs/plink.yaml'
+            'plink'
         log:
             'logs/plink/convert_mapped_to_plink_batch1.log'
         benchmark:
@@ -307,7 +307,7 @@ rule ibis_mapping:
     params:
         genetic_map_GRCh37=expand(GENETIC_MAP_GRCH37,chrom=CHROMOSOMES)
     conda:
-        '../envs/ibis.yaml'
+        'ibis'
     output:
         'preprocessed/data_mapped.bim'
     log:
diff --git a/rules/relatives.smk b/rules/relatives.smk
index 46952a80..0ac685a9 100644
--- a/rules/relatives.smk
+++ b/rules/relatives.smk
@@ -11,7 +11,7 @@ rule run_king:
         kin = "king/data"
     threads: workflow.cores
     conda:
-        "../envs/king.yaml"
+        "king"
     log:
         "logs/king/run_king.log"
     benchmark:
@@ -41,7 +41,7 @@ rule run_king:
 rule index_input:
     input: "preprocessed/data.vcf.gz"
     output: "preprocessed/data.vcf.gz.csi"
-    conda: "../envs/bcftools.yaml"
+    conda: "bcftools"
     shell: "bcftools index -f {input}"
 
 rule index_and_split:
@@ -50,7 +50,7 @@ rule index_and_split:
         index="preprocessed/data.vcf.gz.csi"
     output: "vcf/imputed_chr{chrom}.vcf.gz"
     conda:
-        "../envs/bcftools.yaml"
+        "bcftools"
     # TODO: because "The option is currently used only for the compression of the output stream"
     log:
         "logs/vcf/index_and_split-{chrom}.log"
@@ -72,7 +72,7 @@ rule vcf_to_ped:
     params:
         zarr="zarr/imputed_chr{chrom}.zarr"
     conda:
-        "../envs/vcf_to_ped.yaml"
+        "vcf_to_ped"
     log:
         "logs/ped/vcf_to_ped-{chrom}.log"
     benchmark:
@@ -87,7 +87,7 @@ rule interpolate:
         cmmap=CMMAP
     output: "cm/chr{chrom}.cm.map"
     conda:
-        "../envs/plink.yaml"
+        "plink"
     log:
         "logs/cm/interpolate-{chrom}.log"
     benchmark:
@@ -132,7 +132,7 @@ rule merge_ibd_segments:
         true_ibd='pedsim/simulated/data.seg' # it is in the params because in the case of true data we do not have this information
     output:
         ibd='ibd/merged_ibd.tsv'
-    conda: "../envs/evaluation.yaml"
+    conda: "evaluation"
     script:
         '../scripts/merge_ibd.py'
 
@@ -142,7 +142,7 @@ rule ersa:
     output:
         "ersa/relatives.tsv"
     conda:
-        "../envs/ersa.yaml"
+        "ersa"
     log:
         "logs/ersa/ersa.log"
     benchmark:
@@ -170,6 +170,6 @@ rule merge_king_ersa:
     params:
         cm_dir='cm'
     output: "results/relatives.tsv"
-    conda: "../envs/evaluation.yaml"
+    conda: "evaluation"
     log: "logs/merge/merge-king-ersa.log"
     script: "../scripts/merge_king_ersa.py"
diff --git a/rules/relatives_ibis.smk b/rules/relatives_ibis.smk
index ce0ce40a..be3f7c60 100644
--- a/rules/relatives_ibis.smk
+++ b/rules/relatives_ibis.smk
@@ -8,7 +8,7 @@ rule ibis:
         fam = "preprocessed/data.fam",
         bim = "preprocessed/data_mapped.bim"
     conda:
-        "../envs/ibis.yaml"
+        "ibis"
     output:
         ibd = "ibis/merged_ibis.seg"
     log:
@@ -35,7 +35,7 @@ if config.get('weight_mask'):
             ibd = rules.ibis.output.ibd,
             script = os.path.join(SNAKEFILE_FOLDER, '../weight/apply_weight_mask.py')
         conda:
-            '../envs/weight-mask.yaml'
+            'weight-mask'
         output:
             ibd = os.path.join(WEIGHTED_IBD_SEGMENTS_FOLDER, 'ibis_weighted.seg'),
         params:
@@ -61,7 +61,7 @@ checkpoint transform_ibis_segments:
     log:
         "logs/ibis/transform_ibis_segments.log"
     conda:
-        "../envs/evaluation.yaml"
+        "evaluation"
     script:
         "../scripts/transform_ibis_segments.py"
 
@@ -78,7 +78,7 @@ rule ersa:
     output:
         "ersa/relatives.tsv"
     conda:
-        "../envs/ersa.yaml"
+        "ersa"
     log:
         "logs/ersa/ersa.log"
     benchmark:
@@ -115,6 +115,6 @@ rule postprocess_ersa:
         ibd=rules.ibis.output['ibd'],
         ersa=rules.ersa.output[0]
     output: "results/relatives.tsv"
-    conda: "../envs/evaluation.yaml"
+    conda: "evaluation"
     log: "logs/merge/postprocess-ersa.log"
     script: "../scripts/postprocess_ersa.py"
diff --git a/rules/relatives_ibis_king.smk b/rules/relatives_ibis_king.smk
index 528600ce..8c1f9783 100644
--- a/rules/relatives_ibis_king.smk
+++ b/rules/relatives_ibis_king.smk
@@ -15,7 +15,7 @@ rule run_king:
         kin="king/data"
     threads: workflow.cores
     conda:
-        "../envs/king.yaml"
+        "king"
     log:
         "logs/king/run_king.log"
     benchmark:
@@ -48,7 +48,7 @@ rule ibis:
         fam="preprocessed/data.fam",
         bim="preprocessed/data_mapped.bim"
     conda:
-        "../envs/ibis.yaml"
+        "ibis"
     output:
         ibd     = "ibis/merged_ibis.seg"
     log:
@@ -75,7 +75,7 @@ if config.get('weight_mask'):
             ibd = rules.ibis.output.ibd,
             script = os.path.join(SNAKEFILE_FOLDER, '../weight/apply_weight_mask.py')
         conda:
-            '../envs/weight-mask.yaml'
+            'weight-mask'
         output:
             ibd = os.path.join(WEIGHTED_IBD_SEGMENTS_FOLDER, 'ibis_weighted.seg'),
         params:
@@ -101,7 +101,7 @@ checkpoint transform_ibis_segments:
     log:
         "logs/ibis/transform_ibis_segments.log"
     conda:
-        "../envs/evaluation.yaml"
+        "evaluation"
     script:
         "../scripts/transform_ibis_segments.py"
 
@@ -118,7 +118,7 @@ rule ersa:
     output:
         "ersa/relatives.tsv"
     conda:
-        "../envs/ersa.yaml"
+        "ersa"
     log:
         "logs/ersa/ersa.log"
     benchmark:
@@ -157,7 +157,7 @@ rule split_map:
     params:
         cm_dir='cm'
     conda:
-        "../envs/evaluation.yaml"
+        "evaluation"
     script:
         "../scripts/split_map.py"
 
@@ -172,6 +172,6 @@ rule merge_king_ersa:
     params:
         cm_dir='cm'
     output: "results/relatives.tsv"
-    conda: "../envs/evaluation.yaml"
+    conda: "evaluation"
     log: "logs/merge/merge-king-ersa.log"
     script: "../scripts/merge_king_ersa.py"
diff --git a/workflows/bundle/Snakefile b/workflows/bundle/Snakefile
index aad02a8a..a03388ce 100644
--- a/workflows/bundle/Snakefile
+++ b/workflows/bundle/Snakefile
@@ -38,7 +38,7 @@ if full:
             refHaps = expand(REF_HAPS, chrom=CHROMOSOMES),
             phased_vcf = expand(PHASED_VCF, chrom=CHROMOSOMES)
         conda:
-            "../../envs/download.yaml"
+            "download"
         log:
             "logs/ref/download_bundle.log"
         shell:
@@ -65,7 +65,7 @@ else:
             pedsim_map = PEDSIM_MAP,
             affymetrix_chip = AFFYMETRIX_CHIP
         conda:
-            "../../envs/download.yaml"
+            "download"
         log:
             "logs/ref/download_bundle.log"
         shell:
diff --git a/workflows/pedsim/Snakefile b/workflows/pedsim/Snakefile
index 64a4efc6..5c25f51c 100644
--- a/workflows/pedsim/Snakefile
+++ b/workflows/pedsim/Snakefile
@@ -54,7 +54,7 @@ rule merge_background:
     params:
         list='pedsim/phased/phased.merge.list'
     conda:
-        '../../envs/bcftools.yaml'
+        'bcftools'
     shell:
         """
             # for now just skip empty files
@@ -86,7 +86,7 @@ rule simulate:
         prefix='pedsim/simulated/data',
         seed=simulation_seed
     conda:
-        '../../envs/ped-sim.yaml'
+        'ped-sim'
     shell:
         """
             pedsim -d {input._def} -m {input._map} -i {input.bg} \
@@ -101,7 +101,7 @@ rule shuffle_phase:
         params:
             plink='plink/data_shuffled',
             vcf='pedsim/simulated/data_shuffled'
-        conda: '../../envs/plink.yaml'
+        conda: 'plink'
         shell:
             """
                 plink --vcf {input.vcf} --make-bed --out {params.plink}
@@ -118,7 +118,7 @@ rule postprocess:
         vcf='input.vcf.gz',
         fam='pedsim/simulated/reheaded_data.fam'
     conda:
-        '../../envs/postprocess.yaml'
+        'postprocess'
     script:
         '../../scripts/postprocess.py'
 
@@ -149,6 +149,6 @@ rule evaluate_accuracy:
     log:
         'logs/evaluation/accuracy.log'
     conda:
-        '../../envs/evaluation.yaml'
+        'evaluation'
     script:
          '../../scripts/evaluate.py'
diff --git a/workflows/preprocess_vcf/Snakefile b/workflows/preprocess_vcf/Snakefile
index af5c768d..fedc3b2e 100644
--- a/workflows/preprocess_vcf/Snakefile
+++ b/workflows/preprocess_vcf/Snakefile
@@ -28,7 +28,7 @@ rule recode_vcf:
     input: vcf='input.vcf'
     output: vcf = "vcf/merged_recoded.vcf.gz"
     log: "logs/plink/recode_vcf.log"
-    conda: "../../envs/plink.yaml"
+    conda: "plink"
     shell: "plink --vcf {input.vcf} --chr 1-22 --snps-only just-acgt --output-chr M --not-chr XY,MT --export vcf bgz --out vcf/merged_recoded |& tee {log}"
 
 
@@ -38,7 +38,7 @@ rule liftover:
     output:
         vcf="vcf/merged_lifted.vcf"
     conda:
-        "../envs/liftover.yaml"
+        "liftover"
     log:
         "logs/liftover/liftover.log"
     params:
diff --git a/workflows/reference/Snakefile b/workflows/reference/Snakefile
index c3b1c61f..77b69eda 100644
--- a/workflows/reference/Snakefile
+++ b/workflows/reference/Snakefile
@@ -99,7 +99,7 @@ rule download_GRCh37_fasta:
         GRCh37_fasta = GRCH37_FASTA,
         GRCh37_fasta_fai = GRCH37_FASTA_FAI
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_GRCh37_fasta.log"
     shell:
@@ -133,7 +133,7 @@ rule create_fasta_dict:
     log:
         "logs/ref/create_fasta_dict.log"
     conda:
-        "../../envs/java.yaml"
+        "java"
     shell:
         """
             wget {PICARD_url} --tries 50 -c |& tee -a {log}
@@ -145,7 +145,7 @@ rule download_GENETIC_MAP:
     output:
         GENETIC_MAP = GENETIC_MAP
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_GENETIC_MAP.log"
     shell:
@@ -165,7 +165,7 @@ rule download_genetic_map_GRCh37:
     output:
         genetic_map_GRCh37 = expand(GENETIC_MAP_GRCH37, chrom=CHROMOSOMES)
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_genetic_map_GRCh37.log"
     shell:
@@ -191,7 +191,7 @@ rule download_vcfRef:
     wildcard_constraints:
         chrom="((2[0-2])|(1[0-9])|([1-9]))" # all numbers from 1 to 22
     conda:
-        "../../envs/download.yaml"
+        "download"
     threads:
         workflow.cores
     log:
@@ -222,7 +222,7 @@ rule make_refHaps:
     wildcard_constraints:
         chrom="((2[0-2])|(1[0-9])|([1-9]))" # all numbers from 1 to 22
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/make_refHaps{chrom}.log"
     threads:
@@ -241,7 +241,7 @@ rule download_lift_chain:
     output:
         lift_chain = LIFT_CHAIN
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_lift_chain.log"
     shell:
@@ -265,7 +265,7 @@ rule download_cmmap:
     output:
         cmmap = expand(CMMAP, chrom=CHROMOSOMES)
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_cmmap.log"
     shell:
@@ -289,7 +289,7 @@ rule download_SITE_1000GENOME:
     output:
         SITE_1000GENOME=SITE_1000GENOME
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_SITE_1000GENOME.log"
     shell:
@@ -313,7 +313,7 @@ rule download_affymetrix_chip:
     output:
         affymetrix_chip=AFFYMETRIX_CHIP
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_affymetrix_chip.log"
     shell:
@@ -333,7 +333,7 @@ rule intersect:
         hd_genotype_chip=AFFYMETRIX_CHIP,
         vcfRef=REF_VCF
     output: PHASED_VCF
-    conda: '../../envs/bcftools.yaml'
+    conda: 'bcftools'
     shell:
         """
             bcftools isec -n=2 -w1 -r {wildcards.chrom} \
@@ -345,7 +345,7 @@ rule download_pedsim_map:
     output:
         pedsim_map=PEDSIM_MAP
     conda:
-        "../../envs/download.yaml"
+        "download"
     log:
         "logs/ref/download_pedsim_map.log"
     shell:
diff --git a/workflows/remove_relatives/Snakefile b/workflows/remove_relatives/Snakefile
index 94565585..f5148ad2 100644
--- a/workflows/remove_relatives/Snakefile
+++ b/workflows/remove_relatives/Snakefile
@@ -51,7 +51,7 @@ rule intersect:
         hd_genotype_chip=AFFYMETRIX_CHIP,
         vcfRef=REF_VCF
     output: "phased/chr{chrom}.phased.vcf.gz"
-    conda: "../../envs/bcftools.yaml"
+    conda: "bcftools"
     shell:
         """
             bcftools isec -n=2 -w1 -r {wildcards.chrom} -O z -o {output} {input.vcfRef} {input.hd_genotype_chip}
@@ -66,7 +66,7 @@ rule merge_background:
     params:
         list="phased/phased.merge.list"
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """
             # for now just skip empty files
@@ -96,7 +96,7 @@ rule clean_relatives:
     output:
         remove_list = temp("remove_list.txt")
     conda:
-        "../../envs/remove_relatives.yaml"
+        "remove_relatives"
     script:
         "../../scripts/remove_relatives.py"
 
@@ -110,7 +110,7 @@ rule create_chip:
     params:
         list="pedsim/phased/phased.merge.list"
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """
             bcftools view {input.background} --force-samples --samples-file {input.remove_list} -O z -o {output.back}
diff --git a/workflows/simbig/Snakefile b/workflows/simbig/Snakefile
index 7932aa1f..ef0c6791 100644
--- a/workflows/simbig/Snakefile
+++ b/workflows/simbig/Snakefile
@@ -73,7 +73,7 @@ rule intersect:
     output:
         temp("pedsim/phased/chr{chrom}.phased.vcf.gz")
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """
             bcftools isec -n=2 -w1 -r {wildcards.chrom} -O z -o {output} {input.vcfRef} {input.hd_genotype_chip}
@@ -88,7 +88,7 @@ rule merge_background:
     params:
         list="pedsim/phased/phased.merge.list"
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """
             # for now just skip empty files
@@ -116,7 +116,7 @@ rule split_chip:
     output:
         expand("background/segment{runs}.vcf.gz", runs = list(range(NUM_RUNS)))
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     script:
         "../../scripts/split_chip.py"
 
@@ -129,7 +129,7 @@ rule simulate:
         temp('gen{runs}/data{runs}.vcf.gz'),
         temp('gen{runs}/data{runs}.seg')
     conda:
-        "../../envs/ped-sim.yaml"
+        "ped-sim"
     shell:
         """
             pedsim -d gen{wildcards.runs}/params/relatives_big.def -m {input._map} -i segment{wildcards.runs}.vcf.gz -o gen{wildcards.runs}/data{wildcards.runs} --intf {input.intf} --fam
@@ -141,7 +141,7 @@ rule convert:
     output:
         temp("gen{runs}/data4merge{runs}.vcf.gz")
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """
             bcftools convert gen{wildcards.runs}/data{wildcards.runs}.vcf.gz -O z -o  gen{wildcards.runs}/data4merge{wildcards.runs}.vcf.gz
@@ -153,7 +153,7 @@ rule index:
     output:
         temp("gen{runs}/data4merge{runs}.vcf.gz.csi")
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """
             bcftools index -f gen{wildcards.runs}/data4merge{wildcards.runs}.vcf.gz
@@ -167,7 +167,7 @@ rule merge:
         "generated.vcf.gz",
         "generated.vcf.gz.csi"
     conda:
-        "../../envs/bcftools.yaml"
+        "bcftools"
     shell:
         """  
             bcftools merge --merge id {input.samples} -O z -o generated.vcf.gz
diff --git a/workflows/weight/Snakefile b/workflows/weight/Snakefile
index 7c60c5fe..53f7bee8 100644
--- a/workflows/weight/Snakefile
+++ b/workflows/weight/Snakefile
@@ -25,7 +25,7 @@ rule ibis_ibd_segment_detection:
         fam = 'preprocessed/data.fam',
         bim = 'preprocessed/data_mapped.bim'
     conda:
-        '../../envs/ibis.yaml'
+        'ibis'
     output:
         ibd = IBIS_OUTPUT_PREFIX + '.seg'
     log:
@@ -50,7 +50,7 @@ rule compute_weight_mask:
         ibd = rules.ibis_ibd_segment_detection.output.ibd,
         script = os.path.join(SNAKEFILE_FOLDER, '../../weight/compute_weight_mask.py')
     conda:
-        '../../envs/weight-mask.yaml'
+        'weight-mask'
     output:
         mask = os.path.join(WEIGHT_MASK_FOLDER, 'mask.json'),
         plot = os.path.join(WEIGHT_MASK_FOLDER, 'mask.png')

From 4657712641cdaf81d0e8714acbb4d9b3244874c3 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Wed, 13 Jul 2022 14:55:13 +0000
Subject: [PATCH 35/56] [GRAPE-125] Extended runner's time-out time

---
 .github/workflows/pytest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 8bacfdea..0535f8c9 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -13,6 +13,7 @@ jobs:
   test:
     # Self-hosted runner
     runs-on: self-hosted
+    timeout-minutes: 1000
     # if: |
     #   !github.event.pull_request.head.repo.fork &&
     #   github.head_ref == 'develop'

From d81b4987e0221f2c8eb00901564632d5265dd98b Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Wed, 13 Jul 2022 21:30:12 +0000
Subject: [PATCH 36/56] [GRAPE-125] Changed AADR_SAMPLES_FILEPATH

---
 test/test.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test.py b/test/test.py
index 7d8ff3c9..f5b3e6be 100644
--- a/test/test.py
+++ b/test/test.py
@@ -27,7 +27,7 @@
 AADR_VCF = os.path.join(CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'aadr.reheaded.vcf.gz')
 METRICS_FILEPATH = 'results/metrics.tsv'
 RELATIVES_FILEPATH = 'results/relatives.tsv'
-AADR_SAMPLES_FILEPATH = os.path.join(CONTAINER_TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
+AADR_SAMPLES_FILEPATH = os.path.join(TESTING_REAL_DATA_DIRECTORY, 'aadr_samples.csv')
 
 
 def _download_test_data(test_data_directory):
@@ -129,7 +129,7 @@ def test_data_directory():
             actual_content[relative_path] = os.path.getsize(filepath)
 
     if actual_content != content:
-        print('\nCurrent test data files seem not match "test_data.json", new test data archive will be downloaded!')
+        print('\nCurrent test data files does not match "test_data.json", new test data archive will be downloaded!')
         if not _download_test_data(TESTING_REAL_DATA_DIRECTORY):
             raise Exception('Test data archive download failed!')
 

From 751829aa0c91cc29f885f46b36bf0cb706f6b878 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Mon, 18 Jul 2022 16:46:44 +0300
Subject: [PATCH 37/56] [GRAPE-125] Small fixes

---
 test/test.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/test/test.py b/test/test.py
index f5b3e6be..84860d5f 100644
--- a/test/test.py
+++ b/test/test.py
@@ -80,7 +80,7 @@ def _read_samples_file(filepath):
 def _read_relatives_file(filepath):
     relatives = []
     with open(filepath, 'r') as relatives_file:
-        reader = csv.DictReader(relatives_file, delimiter="\t")
+        reader = csv.DictReader(relatives_file, delimiter='\t')
         for row in reader:
             relative = (row['id1'], row['id2'])
             relatives.append(relative)
@@ -141,7 +141,7 @@ def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
     reference_directory = ReferenceDirectory(REFERENCE_DIRECTORY)
 
     if not reference_directory.is_valid():
-        print('\nCurrrent reference data files seem not match '
+        print('\nCurrrent reference data seem not to match '
               '"reference_directory_content.json", new reference data archive will be downloaded!')
         command = f'launcher.py reference --use-bundle --ref-directory {CONTAINER_REFERENCE_DIRECTORY} ' \
             '--phase --impute --real-run'
@@ -154,7 +154,7 @@ def reference_directory(docker_client, grape_image) -> ReferenceDirectory:
     return reference_directory
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture(scope='function')
 def working_directory(request):
     utc_timestamp = datetime.utcnow().strftime("%Y%m%d-%H%M%S-utc")
     working_directory_name = '-'.join([request.param, utc_timestamp])
@@ -163,7 +163,7 @@ def working_directory(request):
     yield working_directory_path
 
     # Fixture teardown to remove working directory
-    #shutil.rmtree(working_directory_path)
+    shutil.rmtree(working_directory_path)
 
 
 @pytest.mark.parametrize('working_directory', ['ibis'], indirect=True)
@@ -196,7 +196,7 @@ def test_simulation_ibis(docker_client, grape_image, reference_directory, workin
 
 
 @pytest.mark.parametrize('working_directory', ['ibis-king'], indirect=True)
-def test_simulation_king(docker_client, grape_image, reference_directory, working_directory):
+def test_simulation_ibis_king(docker_client, grape_image, reference_directory, working_directory):
     volumes = {
         reference_directory.path: {'bind': CONTAINER_REFERENCE_DIRECTORY, 'mode': 'ro'},
         working_directory: {'bind': CONTAINER_WORKING_DIRECTORY, 'mode': 'rw'}
@@ -308,4 +308,5 @@ def test_aadr(docker_client, grape_image, reference_directory, working_directory
     for relationship in relatives:
         if aadr_samples[relationship[0]] != aadr_samples[relationship[1]]:
             failed_relations += 1
-    assert failed_relations < 2
\ No newline at end of file
+    assert failed_relations < 2
+    

From 34a9ed271bb7211c3af7a754de53e28474f90086 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Mon, 18 Jul 2022 16:52:58 +0300
Subject: [PATCH 38/56] [GRAPE-125] Returned back all changes and added timeout

---
 .github/workflows/pytest.yml | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0535f8c9..11a2adf4 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -7,17 +7,14 @@ on:
 
   workflow_dispatch:
 
-  push:
-
 jobs:
   test:
     # Self-hosted runner
     runs-on: self-hosted
     timeout-minutes: 1000
-    # if: |
-    #   !github.event.pull_request.head.repo.fork &&
-    #   github.head_ref == 'develop'
-
+    if: |
+      !github.event.pull_request.head.repo.fork &&
+      github.head_ref == 'develop'
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
@@ -27,4 +24,5 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r test/requirements.txt
       - run: |
-          pytest test/test.py
\ No newline at end of file
+          pytest test/test.py
+          

From 0e44a32ffeef07ae04589fee0905526ba6376849 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Tue, 19 Jul 2022 10:19:03 +0300
Subject: [PATCH 39/56] [GRAPE-125] Added shutil import

---
 test/test.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/test.py b/test/test.py
index 84860d5f..34b53e4f 100644
--- a/test/test.py
+++ b/test/test.py
@@ -5,6 +5,7 @@
 import json
 import hashlib
 import tarfile
+import shutil
 
 from datetime import datetime
 from reference_directory import ReferenceDirectory

From 58e3695df66efdc4077770085673199249b9b9e3 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Thu, 21 Jul 2022 14:51:20 +0300
Subject: [PATCH 40/56] [GRAPE-128] Added env name

---
 envs/interpolation.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/envs/interpolation.yaml b/envs/interpolation.yaml
index 02cd887b..dda559d6 100644
--- a/envs/interpolation.yaml
+++ b/envs/interpolation.yaml
@@ -1,3 +1,4 @@
+name: interpolation
 channels:
     - bioconda
     - conda-forge
@@ -7,4 +8,4 @@ dependencies:
     - samtools==1.9
     - openssl==1.0.2u
     - pandas==1.1.1
-    - numpy==1.19.1
\ No newline at end of file
+    - numpy==1.19.1

From 96fbe84ec356ad876084cfdb83dae2ce0c7c0942 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Thu, 21 Jul 2022 14:52:44 +0300
Subject: [PATCH 41/56] [GRAPE-128] Added env name

---
 envs/postprocess.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/envs/postprocess.yaml b/envs/postprocess.yaml
index 8e45118f..f86389bf 100644
--- a/envs/postprocess.yaml
+++ b/envs/postprocess.yaml
@@ -1,3 +1,4 @@
+name: postprocess
 channels:
     - bioconda
     - conda-forge

From dbcdb6f03e186f0d5a7fb0af5e89510f29d5cfec Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Fri, 18 Nov 2022 13:50:21 +0300
Subject: [PATCH 42/56] [GRAPE-128] Added custom snakemake package

---
 envs/snakemake.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/envs/snakemake.yaml b/envs/snakemake.yaml
index f208aee3..f0e398b5 100644
--- a/envs/snakemake.yaml
+++ b/envs/snakemake.yaml
@@ -15,3 +15,6 @@ dependencies:
   - scikit-bio==0.5.6
   - docutils==0.16
   - mmh3==3.0.0
+  - pip:
+    - "--editable=git+https://github.com/Jahysama/snakemake.git#egg=snakemake"
+

From 99e0645a274142c60ce5aeec05e1020cc4073485 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Fri, 18 Nov 2022 14:22:41 +0300
Subject: [PATCH 43/56] [GRAPE-128] Added comment about custom snakemake

---
 envs/snakemake.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/envs/snakemake.yaml b/envs/snakemake.yaml
index f0e398b5..9f138bf1 100644
--- a/envs/snakemake.yaml
+++ b/envs/snakemake.yaml
@@ -6,7 +6,6 @@ channels:
   - defaults
 dependencies:
   - python>=3.5
-  - snakemake==7.3.8
   - matplotlib==3.3.1
   - pandas==1.1.1
   - numpy==1.19.1
@@ -17,4 +16,6 @@ dependencies:
   - mmh3==3.0.0
   - pip:
     - "--editable=git+https://github.com/Jahysama/snakemake.git#egg=snakemake"
+    #Fork of a snakemake is used here because of not working conda envs inside python scripts
+    #Please check out https://github.com/snakemake/snakemake/pull/1812 for more info
 

From 8206e7a4064f98f9e740ee0b47ed5ccfaf24343c Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <megametagross@outlook.de>
Date: Tue, 22 Nov 2022 22:56:27 +0300
Subject: [PATCH 44/56] [GRAPE-133] Added mmh3 package

---
 envs/evaluation.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/envs/evaluation.yaml b/envs/evaluation.yaml
index 4dbcd7c4..b098fd3d 100644
--- a/envs/evaluation.yaml
+++ b/envs/evaluation.yaml
@@ -6,4 +6,5 @@ dependencies:
     - seaborn==0.10.1
     - matplotlib==3.3.1
     - pandas==1.1.1
-    - pydot==1.4.2
\ No newline at end of file
+    - pydot==1.4.2
+    - mmh3==3.0.0

From 9f6f642917650d9709d29de47edf2d7fe8a8b727 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <megametagross@outlook.de>
Date: Tue, 22 Nov 2022 23:10:18 +0300
Subject: [PATCH 45/56] [GRAPE-134] Added update get-apt

---
 containers/snakemake/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/containers/snakemake/Dockerfile b/containers/snakemake/Dockerfile
index 9af595eb..41195875 100644
--- a/containers/snakemake/Dockerfile
+++ b/containers/snakemake/Dockerfile
@@ -11,7 +11,7 @@ ENV PATH /opt/conda/bin:${PATH}
 ENV LANG C.UTF-8
 ENV SHELL /bin/bash
 
-RUN apt-get install -y wget bzip2 gnupg2 git libgomp1 && \
+RUN apt-get update && apt-get install -y wget bzip2 gnupg2 git libgomp1 && \
     wget -nv https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
     bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniconda3-latest-Linux-x86_64.sh && \

From c35a3da4fe3260e4c64d06525bf31e8bd8c9a5fa Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Wed, 23 Nov 2022 11:02:08 +0300
Subject: [PATCH 46/56] [GRAPE-133] Renamed env to match in snakemake rules

---
 envs/vcf_to_ped.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/envs/vcf_to_ped.yaml b/envs/vcf_to_ped.yaml
index 07c88fe8..e24ca7cd 100644
--- a/envs/vcf_to_ped.yaml
+++ b/envs/vcf_to_ped.yaml
@@ -1,4 +1,4 @@
-name: vcf_to_ped2
+name: vcf_to_ped
 channels:
     - conda-forge
     - defaults

From d847b8a37e55e71ca5f51bddb78e74273acb4efa Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Mon, 19 Dec 2022 13:44:00 +0300
Subject: [PATCH 47/56] [GRAPE-135] Executing pytest with sudo

---
 .github/workflows/pytest.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 11a2adf4..dc7b64b6 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -19,10 +19,9 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
         with:
-          python-version: 3.9
+          python-version: 3.9.13
       - run: |
           python -m pip install --upgrade pip
           pip install -r test/requirements.txt
       - run: |
-          pytest test/test.py
-          
+          sudo env "PATH=$PATH" pytest test/test.py

From 1dbf45ee6abde89c9aa3197dad40abd8a7be1b48 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Mon, 19 Dec 2022 13:45:37 +0300
Subject: [PATCH 48/56] [GRAPE-135] Updated token

---
 test/test_data.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/test_data.json b/test/test_data.json
index bc45fbad..c7b0e4d0 100644
--- a/test/test_data.json
+++ b/test/test_data.json
@@ -4,7 +4,7 @@
       "url": "https://bioinformatics.file.core.windows.net/bundles/test_data.tar.gz",
       "filesize": 3462612,
       "md5": "c497d0e9840d847c9d8d1b050b4e2427",
-      "azure_public_key": "?sv=2020-08-04&ss=f&srt=sco&sp=r&se=2022-08-08T14:35:53Z&st=2021-08-27T06:35:53Z&spr=https&sig=SjxrSn2KBuQYjYgT2ZZTHQ6IOhA%2BRUSvLIgog%2FH2Tnk%3D"
+      "azure_public_key": "?sv=2021-06-08&ss=f&srt=o&sp=r&se=2023-10-24T18:24:45Z&st=2022-10-24T10:24:45Z&spr=https&sig=xcNx9PyZpj5aF2Xi9573oQ5qYq7VqCIlZdayVtq5NOk%3D"
    },
    "content": {
       "aadr.reheaded.vcf.gz": 3556010338,

From 4f03ad456ea77d3e09925d4bf3a5fed50b229e94 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Tue, 20 Dec 2022 10:55:36 +0300
Subject: [PATCH 49/56] [GRAPE-137] Added v1.7 release notes

---
 CHANGELOG.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bbe0f7c4..6fe2e98a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,20 @@
 # Changelog
 
+## [v1.7] - 2022-12-20
+
+### Added
+
+- All conda environments are now built in Dockerfile and Snakemake doesn't need to create them for every workflow run from `.yaml` files.
+- Multiple tests were added, covering all GRAPE flows. Test cases are stored at `grape/test-cases`.
+
+### Changed
+
+- Phased affymetrix chip is now stored within the bundle to speed up the simulation flow, because of this `intersect` rule in `pedsim` simulation workflow was moved to 'reference' downloading workflow.
+
+### Fixed
+
+- Fixed 'ibis' detecting empty IBD segments causing pipeline teardown.
+
 ## [v1.6] - 2022-05-20
 
 ### Added

From 0ddcf11d57c2ed3352b755b53c40e4b186a57fed Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Thu, 12 Jan 2023 12:22:47 +0300
Subject: [PATCH 50/56] [GRAPE-135] Added numpy version (float error)

---
 envs/evaluation.yaml  | 1 +
 envs/weight-mask.yaml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/envs/evaluation.yaml b/envs/evaluation.yaml
index b098fd3d..20700b5d 100644
--- a/envs/evaluation.yaml
+++ b/envs/evaluation.yaml
@@ -8,3 +8,4 @@ dependencies:
     - pandas==1.1.1
     - pydot==1.4.2
     - mmh3==3.0.0
+    - numpy==1.20
diff --git a/envs/weight-mask.yaml b/envs/weight-mask.yaml
index ad42467d..75a38d35 100644
--- a/envs/weight-mask.yaml
+++ b/envs/weight-mask.yaml
@@ -2,6 +2,6 @@ name: weight-mask
 channels:
   - conda-forge
 dependencies:
-  - numpy
+  - numpy==1.20
   - scikit-learn
   - matplotlib

From 464ebd1613a3fadc7ca54d731dee39056cdf63ab Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Thu, 12 Jan 2023 12:25:33 +0300
Subject: [PATCH 51/56] [GRAPE-135] pytest is now runs as root on host by
 default

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index dc7b64b6..e68d16d1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -24,4 +24,4 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r test/requirements.txt
       - run: |
-          sudo env "PATH=$PATH" pytest test/test.py
+          pytest test/test.py

From 56e7d7eef64dc35162b80bfab2817ce7a05d2d68 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Thu, 12 Jan 2023 13:03:58 +0300
Subject: [PATCH 52/56] [HOTFIX] Updated release date

---
 CHANGELOG.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6fe2e98a..2d4ef7ab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## [v1.7] - 2022-12-20
+## [v1.7] - 2023-01-12
 
 ### Added
 
@@ -9,11 +9,11 @@
 
 ### Changed
 
-- Phased affymetrix chip is now stored within the bundle to speed up the simulation flow, because of this `intersect` rule in `pedsim` simulation workflow was moved to 'reference' downloading workflow.
+- Phased affymetrix chip is now stored within the bundle to speed up the simulation flow, because of this `intersect` rule in `pedsim` simulation workflow was moved to `reference` downloading workflow.
 
 ### Fixed
 
-- Fixed 'ibis' detecting empty IBD segments causing pipeline teardown.
+- Fixed `ibis` detecting empty IBD segments causing pipeline teardown.
 
 ## [v1.6] - 2022-05-20
 

From ab1c24d89f6292692216504071609ff6a4802785 Mon Sep 17 00:00:00 2001
From: Egor <megametagross@outlook.de>
Date: Thu, 12 Jan 2023 14:57:18 +0300
Subject: [PATCH 53/56] Revert "Merge branch 'master' into develop"

This reverts commit 80ca645b1c7173a766205b39470dd168618b8222, reversing
changes made to 8f16591e930960c65c4ce3bba6f365943dc9e9a9.
---
 rules/imputation.smk    | 2 +-
 rules/preprocessing.smk | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/rules/imputation.smk b/rules/imputation.smk
index 96262a86..88324e89 100644
--- a/rules/imputation.smk
+++ b/rules/imputation.smk
@@ -135,5 +135,5 @@ rule merge_convert_imputed_to_plink:
         '''
         # please mind a merge step in merge_imputation_filter for germline
         plink --vcf {input} --make-bed --out {params.out} | tee {log}
-        plink --bfile {params.background} --bmerge {params.out} --make-bed --out plink/{wildcards.batch}_merged_imputed |& tee {log}
+        plink --bfile {params.background} --bmerge {params.out} --make-bed --out plink/{batch}_merged_imputed |& tee {log}
         '''
diff --git a/rules/preprocessing.smk b/rules/preprocessing.smk
index a3066375..aae06673 100644
--- a/rules/preprocessing.smk
+++ b/rules/preprocessing.smk
@@ -109,7 +109,7 @@ if assembly == 'hg38':
             mem_mb=_mem_gb_for_ram_hungry_jobs() * 1024
         shell:
             '''
-               picard -Xmx{params.mem_gb}g LiftoverVcf -WARN_ON_MISSING_CONTIG true -MAX_RECORDS_IN_RAM 5000 -I {input.vcf} -O {output.vcf} -CHAIN {LIFT_CHAIN} -REJECT vcf/chr{wildcards.batch}_rejected.vcf.gz -R {GRCH37_FASTA} |& tee -a {log}
+               java -Xmx{params.mem_gb}g -jar /picard/picard.jar LiftoverVcf WARN_ON_MISSING_CONTIG=true MAX_RECORDS_IN_RAM=5000 I={input.vcf} O={output.vcf} CHAIN={LIFT_CHAIN} REJECT=vcf/chr{wildcards.batch}_rejected.vcf.gz R={GRCH37_FASTA} |& tee -a {log}
             '''
 else:
     rule copy_liftover:

From 6e69509f174d278dc73f728a026e8e5fb85ec5ac Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Thu, 12 Jan 2023 15:25:09 +0300
Subject: [PATCH 54/56] [HOTFIX] Added pr reopening trigger

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index e68d16d1..bb77b418 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -3,7 +3,7 @@ name: Run Python Tests
 on:
   pull_request:
     branches: [ master ]
-    types: [ opened ]
+    types: [ opened, reopened ]
 
   workflow_dispatch:
 

From 63da78287a919eec7d7099d8eab889b6ee5af001 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Thu, 12 Jan 2023 23:32:21 +0300
Subject: [PATCH 55/56] [HOTFIX] Added numpy version (float error)

---
 envs/vcf_to_ped.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/envs/vcf_to_ped.yaml b/envs/vcf_to_ped.yaml
index e24ca7cd..a7171a79 100644
--- a/envs/vcf_to_ped.yaml
+++ b/envs/vcf_to_ped.yaml
@@ -4,3 +4,4 @@ channels:
     - defaults
 dependencies:
     - scikit-allel==1.3.2
+    - numpy==1.20

From ba5e16c734f119f31753d28aab87d586d140c284 Mon Sep 17 00:00:00 2001
From: Egor Kosaretskiy <52824960+Jahysama@users.noreply.github.com>
Date: Fri, 13 Jan 2023 19:11:39 +0300
Subject: [PATCH 56/56] [HOTFIX] Fixed bug from issue #88 master

---
 rules/imputation.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rules/imputation.smk b/rules/imputation.smk
index 88324e89..96262a86 100644
--- a/rules/imputation.smk
+++ b/rules/imputation.smk
@@ -135,5 +135,5 @@ rule merge_convert_imputed_to_plink:
         '''
         # please mind a merge step in merge_imputation_filter for germline
         plink --vcf {input} --make-bed --out {params.out} | tee {log}
-        plink --bfile {params.background} --bmerge {params.out} --make-bed --out plink/{batch}_merged_imputed |& tee {log}
+        plink --bfile {params.background} --bmerge {params.out} --make-bed --out plink/{wildcards.batch}_merged_imputed |& tee {log}
         '''