Merge pull request #253 from nschcolnicov/fix_mkfastq

Fix mkfastq
nf-core · Aug 19, 2024 · da9d837 · da9d837
2 parents 24edd51 + 452e918
commit da9d837
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Showing 8 changed files with 103 additions and 45 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -203,7 +203,14 @@ process {
                 //Gather fastqs
                 path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "**/outs/fastq_path/**.fastq.gz",
+                pattern: "**/outs/fastq_path/**/*.fastq.gz",
+                saveAs: {filename -> filename.split("/")[-1] }
+            ],
+            [
+                //Gather undetermined fastqs
+                path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}/undetermined" : "${params.outdir}/${meta.id}/undetermined" },
+                mode: params.publish_dir_mode,
+                pattern: "**/outs/fastq_path/*.fastq.gz",
                 saveAs: {filename -> filename.split("/")[-1] }
             ]
         ]

diff --git a/conf/test_mkfastq.config b/conf/test_mkfastq.config
@@ -20,7 +20,7 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/mkfastq-samplesheet.csv'
+    input         = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/cellranger_tiny/mkfastq_tiny_samplesheet.csv'
     demultiplexer = 'mkfastq'
-    skip_tools    = 'samshee'
+    skip_tools    = 'samshee,falco'
 }
diff --git a/modules.json b/modules.json
@@ -22,19 +22,14 @@
                     },
                     "cellranger/mkfastq": {
                         "branch": "master",
-                        "git_sha": "d89faad13503f47372b8706008f7cdb2c4f1d859",
+                        "git_sha": "61123e49c6034920eb6f312ad71e4815a7853257",
                         "installed_by": ["modules"]
                     },
                     "checkqc": {
                         "branch": "master",
                         "git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731",
                         "installed_by": ["modules"]
                     },
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
-                        "installed_by": ["modules"]
-                    },
                     "falco": {
                         "branch": "master",
                         "git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5",

diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf
diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test
diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap
diff --git a/tests/pipeline/mkfastq.nf.test b/tests/pipeline/mkfastq.nf.test
@@ -18,25 +18,32 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
-                { assert workflow.trace.succeeded().size() == 7 },
+                { assert workflow.trace.succeeded().size() == 10 },
                 // How many directories were produced?
                 {assert path("${outputDir}").list().size() == 6},
                 // How many files were produced?
-                {assert path("$outputDir/220422_M11111_0222_000000000-K9H97_mkfastq/").list().size() == 2},
+                {assert path("$outputDir/cellranger-tiny-bcl-simple/").list().size() == 2},
                 {assert path("$outputDir/multiqc/").list().size() == 3},
                 {assert path("$outputDir/pipeline_info/").list().size() == 5},
                 // File assertions: Files that should be exactly the same with every pipeline execution.
                 {assert snapshot(
                     //Check output files
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_summary.txt"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_report.html").exists(),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_R1_001.fastq.gz"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_fastqc_data.txt"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.json"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.html").exists(),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz.md5"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz"),
-                    path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/InterOp/IndexMetricsOut.bin")
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz.md5"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz.md5"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz.md5"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R1_001.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R2_001.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_I1_001.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"),
+                    path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin")
                 ).match("file_assertions_mkfastq")}
             )
         }

diff --git a/tests/pipeline/mkfastq.nf.test.snap b/tests/pipeline/mkfastq.nf.test.snap
@@ -1,30 +1,37 @@
 {
     "software_versions": {
         "content": [
-            "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1dev}}"
+            "{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.0"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-08-02T20:09:53.707554042"
+        "timestamp": "2024-08-15T17:36:35.551329"
     },
     "file_assertions_mkfastq": {
         "content": [
-            "Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6",
+            "test_sample_S1_L001_1.fastp.fastq.gz:md5,b348491a3b1afa096fde514dbdf55215",
+            "test_sample_S1_L001_1.fastp.fastq.gz.md5:md5,43d7882f3aaae47b56df56da6c802236",
+            "test_sample_S1_L001_2.fastp.fastq.gz:md5,1c60f1f3958b8b2b0255b9fae6df0b3d",
+            "test_sample_S1_L001_2.fastp.fastq.gz.md5:md5,01d742cc56639c476b0bac0c094eba4b",
+            "test_sample_S1_L001_I1_001.fastp.fastq.gz.md5:md5,82e397b4a2418f27269a30f6ca0e349e",
+            "test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453",
+            "test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc",
+            "test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2",
+            "Undetermined_S0_L001_I1_001.fastq.gz:md5,c93946d67bdb1d5b2ab955fd1dc9cb31",
+            "Undetermined_S0_L001_R1_001.fastq.gz:md5,faa79ce215ae72fdc3375cda066c6757",
+            "Undetermined_S0_L001_R2_001.fastq.gz:md5,d8955db4dfbf7aee89b6bdc3b7629f8f",
             true,
-            "Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b",
-            "Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7",
-            "Sample1_S1_L001.fastp.json:md5,ed62c667631b03f5fd3b50454322b423",
             true,
-            "Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c",
-            "Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373",
-            "IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf"
+            "test_sample_S1_L001.fastp.json:md5,f616058446c5822797048ea6c5d2393d",
+            "test_sample_S1_L001_I1_001.fastp.json:md5,42cad4ed99a3d577f100017cbe11d711",
+            "IndexMetricsOut.bin:md5,e2ac28695537336b53a509f48e93ed1f"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-23T23:50:42.910185053"
+        "timestamp": "2024-08-15T17:54:45.551098"
     }
-}
+}