From ec5df508f7c745f8106e7e6ee48e76a823378f21 Mon Sep 17 00:00:00 2001 From: Junjun Zhang Date: Thu, 25 Jun 2020 09:44:21 -0400 Subject: [PATCH] cleaned up test data, added new test for FQ input --- dna-seq-alignment/tests/test-local_fq.json | 16 ++ ...75-e94d15ba291a.sequencing_experiment.json | 126 +++++++++++++ tests/data/C0HVY.2_r1.fq | 112 ------------ tests/data/C0HVY.2_r1.fq.gz | Bin 0 -> 2040 bytes tests/data/C0HVY.2_r2.fq | 112 ------------ tests/data/C0HVY.2_r2.fq.gz | Bin 0 -> 2042 bytes tests/data/C0HVY_2.lane.bam | Bin 3990 -> 0 bytes tests/data/D0RE2.1_r1.fq | 128 -------------- tests/data/D0RE2.1_r1.fq.gz | Bin 0 -> 2309 bytes tests/data/D0RE2.1_r2.fq | 128 -------------- tests/data/D0RE2.1_r2.fq.gz | Bin 0 -> 2365 bytes tests/data/D0RE2_1.lane.bam | Bin 4551 -> 0 bytes tests/data/D0RH0.2_r1.fq | 100 ----------- tests/data/D0RH0.2_r1.fq.gz | Bin 0 -> 1872 bytes tests/data/D0RH0.2_r2.fq | 100 ----------- tests/data/D0RH0.2_r2.fq.gz | Bin 0 -> 1894 bytes tests/data/D0RH0_2.lane.bam | Bin 3672 -> 0 bytes tests/data/HCC1143.3.20190726.wgs.grch38.bam | Bin 13210 -> 0 bytes .../HCC1143.3.20190726.wgs.grch38.bam.bai | Bin 352 -> 0 bytes ...CC1143_BAM_INPUT.3.20190812.wgs.grch38.bam | Bin 13197 -> 0 bytes ...43_BAM_INPUT.3.20190812.wgs.grch38.bam.bai | Bin 352 -> 0 bytes ...0812.wgs.grch38.bam.duplicates-metrics.txt | 108 ------------ ...CC1143_BAM_INPUT.3.20190814.wgs.grch38.bam | Bin 13198 -> 0 bytes ...43_BAM_INPUT.3.20190814.wgs.grch38.bam.bai | Bin 352 -> 0 bytes ...0814.wgs.grch38.bam.duplicates-metrics.txt | 108 ------------ ...C1143_BAM_INPUT.3.20190814.wgs.grch38.cram | Bin 10071 -> 0 bytes ..._BAM_INPUT.3.20190814.wgs.grch38.cram.crai | Bin 64 -> 0 bytes .../PCSI_0115_Pa_P.copynumber.caveman.vcf.gz | 0 ...SI_0115_Pa_P.copynumber.caveman.vcf.gz.tbi | 0 ...115_Pa_P.tumour.sequencing_experiment.json | 29 --- ...Pa_P.wgs.tumour.sequencing_experiment.json | 29 --- ...I_0115_Pa_P_vs_PCSI_0115_Ly_R.annot.vcf.gz | 0 ...15_Pa_P_vs_PCSI_0115_Ly_R.annot.vcf.gz.tbi | 0 ...Pa_P_vs_PCSI_0115_Ly_R.flagged.muts.vcf.gz | 0 ..._vs_PCSI_0115_Ly_R.flagged.muts.vcf.gz.tbi | 0 ...0115_Pa_P_vs_PCSI_0115_Ly_R.flagged.vcf.gz | 0 ..._Pa_P_vs_PCSI_0115_Ly_R.flagged.vcf.gz.tbi | 0 .../aligned_bam.PCSI_0115_Ly_R.normal.json | 73 -------- .../aligned_bam.PCSI_0115_Pa_P.tumour.json | 73 -------- tests/data/broad-mutect2.snv-indel.vcf.gz | 0 tests/data/broad-mutect2.snv-indel.vcf.gz.tbi | 0 tests/data/dna_alignment.test.json | 103 ----------- tests/data/experiment-fq.tsv | 2 - tests/data/experiment-fq.v2.fake-PACA-CA.tsv | 2 - tests/data/experiment-fq.v2.tsv | 2 - tests/data/experiment-lgc-bam.v2.tsv | 2 - tests/data/experiment.tsv | 2 - tests/data/experiment.v2.fake-PACA-CA.tsv | 2 - tests/data/experiment.v2.tsv | 2 - tests/data/file-fq.tsv | 7 - tests/data/file-fq.v2.tsv | 7 - tests/data/file-lgc-bam.v2.tsv | 2 - tests/data/file.tsv | 4 - tests/data/file.v2.tsv | 2 - tests/data/lane_seq_submission.C0HVY_2.json | 41 ----- .../lane_seq_submission.C0HVY_2.lane.bam.json | 35 ---- tests/data/lane_seq_submission.D0RE2_1.json | 41 ----- .../lane_seq_submission.D0RE2_1.lane.bam.json | 35 ---- .../lane_seq_submission.D0RH0_2.lane.bam.json | 35 ---- tests/data/read_group-fq.tsv | 4 - tests/data/read_group-fq.v2.tsv | 4 - tests/data/read_group-lgc-bam.v2.tsv | 2 - tests/data/read_group.tsv | 4 - tests/data/read_group.v2.tsv | 4 - tests/data/rg_ubam.song-analysis.01.json | 68 -------- tests/data/rg_ubam.song-analysis.02.json | 68 -------- tests/data/rg_ubam.song-analysis.03.json | 68 -------- tests/data/seq-exp.bam.metadata.json | 73 -------- tests/data/seq-exp.fq.metadata.json | 113 ------------ tests/data/seq-rg-bam.json | 69 -------- tests/data/seq_exp-fq.payload.json | 136 --------------- tests/data/seq_exp-fq.song-analysis.json | 165 ------------------ tests/data/seq_rg-fq.json | 121 ------------- tests/data/seq_rg.json | 71 -------- tests/data/test_rg_3.bam | Bin 14899 -> 0 bytes tests/data/test_rg_3.bam.bai | 0 76 files changed, 142 insertions(+), 2396 deletions(-) create mode 100644 dna-seq-alignment/tests/test-local_fq.json create mode 100644 tests/data/83185fe5-71cc-4515-bc75-e94d15ba291a.sequencing_experiment.json delete mode 100644 tests/data/C0HVY.2_r1.fq create mode 100644 tests/data/C0HVY.2_r1.fq.gz delete mode 100644 tests/data/C0HVY.2_r2.fq create mode 100644 tests/data/C0HVY.2_r2.fq.gz delete mode 100644 tests/data/C0HVY_2.lane.bam delete mode 100644 tests/data/D0RE2.1_r1.fq create mode 100644 tests/data/D0RE2.1_r1.fq.gz delete mode 100644 tests/data/D0RE2.1_r2.fq create mode 100644 tests/data/D0RE2.1_r2.fq.gz delete mode 100644 tests/data/D0RE2_1.lane.bam delete mode 100644 tests/data/D0RH0.2_r1.fq create mode 100644 tests/data/D0RH0.2_r1.fq.gz delete mode 100644 tests/data/D0RH0.2_r2.fq create mode 100644 tests/data/D0RH0.2_r2.fq.gz delete mode 100644 tests/data/D0RH0_2.lane.bam delete mode 100644 tests/data/HCC1143.3.20190726.wgs.grch38.bam delete mode 100644 tests/data/HCC1143.3.20190726.wgs.grch38.bam.bai delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190812.wgs.grch38.bam delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190812.wgs.grch38.bam.bai delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190812.wgs.grch38.bam.duplicates-metrics.txt delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam.bai delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam.duplicates-metrics.txt delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.cram delete mode 100644 tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.cram.crai delete mode 100644 tests/data/PCSI_0115_Pa_P.copynumber.caveman.vcf.gz delete mode 100644 tests/data/PCSI_0115_Pa_P.copynumber.caveman.vcf.gz.tbi delete mode 100644 tests/data/PCSI_0115_Pa_P.tumour.sequencing_experiment.json delete mode 100644 tests/data/PCSI_0115_Pa_P.wgs.tumour.sequencing_experiment.json delete mode 100644 tests/data/PCSI_0115_Pa_P_vs_PCSI_0115_Ly_R.annot.vcf.gz delete mode 100644 tests/data/PCSI_0115_Pa_P_vs_PCSI_0115_Ly_R.annot.vcf.gz.tbi delete mode 100644 tests/data/PCSI_0115_Pa_P_vs_PCSI_0115_Ly_R.flagged.muts.vcf.gz delete mode 100644 tests/data/PCSI_0115_Pa_P_vs_PCSI_0115_Ly_R.flagged.muts.vcf.gz.tbi delete mode 100644 tests/data/PCSI_0115_Pa_P_vs_PCSI_0115_Ly_R.flagged.vcf.gz delete mode 100644 tests/data/PCSI_0115_Pa_P_vs_PCSI_0115_Ly_R.flagged.vcf.gz.tbi delete mode 100644 tests/data/aligned_bam.PCSI_0115_Ly_R.normal.json delete mode 100644 tests/data/aligned_bam.PCSI_0115_Pa_P.tumour.json delete mode 100644 tests/data/broad-mutect2.snv-indel.vcf.gz delete mode 100644 tests/data/broad-mutect2.snv-indel.vcf.gz.tbi delete mode 100644 tests/data/dna_alignment.test.json delete mode 100644 tests/data/experiment-fq.tsv delete mode 100644 tests/data/experiment-fq.v2.fake-PACA-CA.tsv delete mode 100644 tests/data/experiment-fq.v2.tsv delete mode 100644 tests/data/experiment-lgc-bam.v2.tsv delete mode 100644 tests/data/experiment.tsv delete mode 100644 tests/data/experiment.v2.fake-PACA-CA.tsv delete mode 100644 tests/data/experiment.v2.tsv delete mode 100644 tests/data/file-fq.tsv delete mode 100644 tests/data/file-fq.v2.tsv delete mode 100644 tests/data/file-lgc-bam.v2.tsv delete mode 100644 tests/data/file.tsv delete mode 100644 tests/data/file.v2.tsv delete mode 100644 tests/data/lane_seq_submission.C0HVY_2.json delete mode 100644 tests/data/lane_seq_submission.C0HVY_2.lane.bam.json delete mode 100644 tests/data/lane_seq_submission.D0RE2_1.json delete mode 100644 tests/data/lane_seq_submission.D0RE2_1.lane.bam.json delete mode 100644 tests/data/lane_seq_submission.D0RH0_2.lane.bam.json delete mode 100644 tests/data/read_group-fq.tsv delete mode 100644 tests/data/read_group-fq.v2.tsv delete mode 100644 tests/data/read_group-lgc-bam.v2.tsv delete mode 100644 tests/data/read_group.tsv delete mode 100644 tests/data/read_group.v2.tsv delete mode 100644 tests/data/rg_ubam.song-analysis.01.json delete mode 100644 tests/data/rg_ubam.song-analysis.02.json delete mode 100644 tests/data/rg_ubam.song-analysis.03.json delete mode 100644 tests/data/seq-exp.bam.metadata.json delete mode 100644 tests/data/seq-exp.fq.metadata.json delete mode 100644 tests/data/seq-rg-bam.json delete mode 100644 tests/data/seq_exp-fq.payload.json delete mode 100644 tests/data/seq_exp-fq.song-analysis.json delete mode 100644 tests/data/seq_rg-fq.json delete mode 100644 tests/data/seq_rg.json delete mode 100644 tests/data/test_rg_3.bam delete mode 100644 tests/data/test_rg_3.bam.bai diff --git a/dna-seq-alignment/tests/test-local_fq.json b/dna-seq-alignment/tests/test-local_fq.json new file mode 100644 index 0000000..fe83c5b --- /dev/null +++ b/dna-seq-alignment/tests/test-local_fq.json @@ -0,0 +1,16 @@ +{ + "study_id": "TEST-PR", + "analysis_metadata": "data/83185fe5-71cc-4515-bc75-e94d15ba291a.sequencing_experiment.json", + "sequencing_files": [ + "data/D0RE2.1_r2.fq.gz", + "data/D0RH0.2_r1.fq.gz", + "data/D0RE2.1_r1.fq.gz", + "data/D0RH0.2_r2.fq.gz", + "data/C0HVY.2_r2.fq.gz", + "data/C0HVY.2_r1.fq.gz" + ], + "ref_genome_fa": "reference/tiny-grch38-chr11-530001-537000.fa", + "cpus": 2, + "mem": 2, + "tempdir": "NO_DIR" +} diff --git a/tests/data/83185fe5-71cc-4515-bc75-e94d15ba291a.sequencing_experiment.json b/tests/data/83185fe5-71cc-4515-bc75-e94d15ba291a.sequencing_experiment.json new file mode 100644 index 0000000..c6f068d --- /dev/null +++ b/tests/data/83185fe5-71cc-4515-bc75-e94d15ba291a.sequencing_experiment.json @@ -0,0 +1,126 @@ +{ + "analysisType": { + "name": "sequencing_experiment" + }, + "studyId": "TEST-PR", + "experiment": { + "submitter_sequencing_experiment_id": "TEST_EXP1", + "sequencing_center": "EXT", + "platform": "ILLUMINA", + "platform_model": "HiSeq 2000", + "experimental_strategy": "WGS", + "sequencing_date": "2014-12-12" + }, + "read_group_count": 3, + "read_groups": [ + { + "submitter_read_group_id": "C0HVY.2", + "platform_unit": "74_8a", + "is_paired_end": true, + "file_r1": "C0HVY.2_r1.fq.gz", + "file_r2": "C0HVY.2_r2.fq.gz", + "read_length_r1": 150, + "read_length_r2": 150, + "insert_size": 298, + "sample_barcode": null, + "library_name": "Pond-147580" + }, + { + "submitter_read_group_id": "D0RE2.1", + "platform_unit": "74_8b", + "is_paired_end": true, + "file_r1": "D0RE2.1_r1.fq.gz", + "file_r2": "D0RE2.1_r2.fq.gz", + "read_length_r1": 150, + "read_length_r2": 150, + "insert_size": 298, + "sample_barcode": null, + "library_name": "Pond-147580" + }, + { + "submitter_read_group_id": "D0RH0.2", + "platform_unit": "74_8c", + "is_paired_end": true, + "file_r1": "D0RH0.2_r1.fq.gz", + "file_r2": "D0RH0.2_r2.fq.gz", + "read_length_r1": 150, + "read_length_r2": 150, + "insert_size": 298, + "sample_barcode": null, + "library_name": "Pond-147580" + } + ], + "samples": [ + { + "sampleId": "SA610149", + "specimenId": "SP210129", + "submitterSampleId": "HCC1143_BAM_INPUT", + "matchedNormalSubmitterSampleId": null, + "sampleType": "Total DNA", + "specimen": { + "specimenId": "SP210129", + "donorId": "DO250122", + "submitterSpecimenId": "HCC1143_BAM_INPUT", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Blood derived", + "specimenType": "Cell line - derived from normal" + }, + "donor": { + "donorId": "DO250122", + "studyId": "TEST-PR", + "gender": "Female", + "submitterDonorId": "HCC1143" + } + } + ], + "files": [ + { + "fileName": "C0HVY.2_r1.fq.gz", + "fileSize": 2040, + "fileMd5sum": "64cf635dbc54f53cae2cb03ec8e8471b", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + }, + { + "fileName": "C0HVY.2_r2.fq.gz", + "fileSize": 2042, + "fileMd5sum": "ceb7e66d031cb894fa9d1d3f8da65fc7", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + }, + { + "fileName": "D0RE2.1_r1.fq.gz", + "fileSize": 2309, + "fileMd5sum": "44bea7aa32a1afb68eec24496b608545", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + }, + { + "fileName": "D0RE2.1_r2.fq.gz", + "fileSize": 2365, + "fileMd5sum": "d73b37eca9375258ab42905f7943b1b6", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + }, + { + "fileName": "D0RH0.2_r1.fq.gz", + "fileSize": 1872, + "fileMd5sum": "b90a3c9750db29406f31e9488d5b7e2b", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + }, + { + "fileName": "D0RH0.2_r2.fq.gz", + "fileSize": 1894, + "fileMd5sum": "a407247b584daa078114ab05e6e489be", + "fileType": "FASTQ", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + } + ] +} diff --git a/tests/data/C0HVY.2_r1.fq b/tests/data/C0HVY.2_r1.fq deleted file mode 100644 index c74fd99..0000000 --- a/tests/data/C0HVY.2_r1.fq +++ /dev/null @@ -1,112 +0,0 @@ -@C0HVYACXX120402:2:1102:2628:3832 -CGGGGAGGGCTTCCTGTGTGTGTTTGCCATCAACAACACCAAGTCTTTTGAGGACATCCACCAGTACAGGTGAACC -+ -CCCFFFFFHHHHHJJJGGIIHHIIJIIJJJJJGIIJJJJJJJJGHJJJJJJIJJJHHHHHFFFFEEDEEEDDDDDA -@C0HVYACXX120402:2:1102:17044:93282 -GGCCAGCCTCACGGGGTTCACCTGTACTGGTGGATGTCCTCAAAAGACTTGGTGTTGTTGATGGCAAACACAGATC -+ -@C@FFBDDDDHFHIIIFEHGGIGHDHHGGGDFGEGGHIHIIGIICACGGIG;=FFDDDGHHGHDHDFFFECCEC@? -@C0HVYACXX120402:2:1106:13179:108296 -GGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGGCCCTGGCTA -+ -@@@DD:BDH>ADDDBGGCHAFH?E@:CGCDAFC:?<::?FA9DCHBHGEAFEGE?##################### -@C0HVYACXX120402:2:1106:17358:51705 -AGACAGGGCCACAGCACCATGCAGGGGACCAGGGGCTGCAGCCAGCCCTATCCTGGCTGTGTCCTGGGCTCGCCCG -+ -@@@FFFFFBDHHHGIJIIJJGEEHGHIGHIJCBHHIJIIIDIIIGGHHIGHHHGHEFFFCEECEECDDDDDB=BD9 -@C0HVYACXX120402:2:1107:20854:145640 -AGCTGGATGGTCAGCGCACTCTTGCCCACACCGCCGGCGCCCACCACCACCAGCTTATATTCCGTCATCGCTCCTC -+ -@@CFFFFDFHCFDGGIIGIGGIJIIIJBHGIGIIIJJJHFFDDDDDDDBDDDDDDCCCCCCDDCDDD?CDDDBDCC -@C0HVYACXX120402:2:1108:5651:15094 -GCATCCCCTACATCGAGACCTCGGCCAAGACCCGGCAGGTGAGGCAGCTCTCCACCCCACAGCTAGCCAGGGACCC -+ -?;;?A################### -@C0HVYACXX120402:2:1202:11055:187078 -CACCTCTCAGGGAGCAGATCAAACGGGTGAAGGACTCGGATGACGTGCCCATGGTGCTGGTGGGGAACAAGTGTGA -+ -@@@?DDDADHDDAHHIBEA+AECHHGG?DEGCH@HCEH?@;@FCHCFAGIIIIGHFHEE@@DEA>?BBBC?5>AC@ -@C0HVYACXX120402:2:1204:10977:133698 -TGAGAGGTACCAGGGAGAGGCTGGCTGTGTGAACTCCCCCCACGGAAGGTCCTGAGGGGGTCCCTGAGCCCTGTCC -+ -?@@FFFF=CFHHFIGIJIIGIHIJCGEF>DEGFDFGIJIIJHIIJG;=E=BC@BCC?ABD8;ABCA@BBB@8 -@C0HVYACXX120402:2:1208:12152:40423 -GGAGTCGGGAGCTTCGGGCCAGGCAAGGCTTGATCCCACAGCAGGGAGCCCCTCACCCAGGCAGGCGGCCACAGGC -+ -@@CFDDDFFHHDFGIIIIFIIIGGIGECBBFFEGIIIEGIEABBDDDDCED@BDBB@?A:@:@CA@CD899<@B0 -@C0HVYACXX120402:2:1304:10709:146499 -GTGCAGCCAGGTCACACTTGTTCCCCACCAGCACCATGGGCACGTCATCCGAGTCCTTCACCCGTTTGATCTGCTC -+ -@@@D?:DDHDBHFHB@BFD?CCE@FHIE@=EEBHEBFDHBDEGG@FGG<87@FH>4=@E@=7==5@??;;>ACCC; -@C0HVYACXX120402:2:1304:16584:143472 -CACAGCAGGGAGCCCCTCACCCAGGCAGGCGGCCACAGGCCGGTCCCTCCTGATCCCATCCCTCCTTTCCCAGGGA -+ -@CCFFFFFHHAHHIIIJJJJJJJJJIIJJIIIGHGGEAHEHFD=@DDCCB?>CCCACCCCDD@CDACDCDD3:?B< -@C0HVYACXX120402:2:1305:8052:134605 -CTCGTCTCAGCACCCCAGGAGAGGAGGGGGCATGAGGGGCATGAGAGGTACCAGGGAGAGGCTGGCTGTGTGAACT -+ -CCCFFFFEHHGHHJJBIIIHHFFGEGGGGIIEHIGHGCHFEHEFFECC>CE@CC?@B88??BBDB7@@ -@C0HVYACXX120402:2:1305:13049:61181 -GAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGGGGG -+ -@CCFFFFFHFHHGJJFIGEEBFDGEGIHI=F@ECHBGD==FFBCHED@FGGHIHEHDFDBDD8############# -@C0HVYACXX120402:2:1305:13225:67333 -CTCCCCCCACGGAAGGTCCTGAGGGGGTCCCTGAGCCCTGTCCTCCTGCAGGATTCCTACCGGAAGCAGGTGGTCA -+ -CCCFFFFFHHHHHJJJIJJJJJJJJJJFHIJJJJJHHHHHFFFFFEDEEEDDDDDDFDDDDDDDDDDDDD?CB0@@ -@C0HVYACXX120402:2:2105:6582:86372 -GCATGTACTGGTCCCGCATGGCGCTGTACTCCTCCTGGCCGGAGGTATCCAGGATGTCCAACAGGCACGTCTCCCC -+ -CCCFDFFFGHFHHGDGGHJFGGHIJFBHIJGEGFHGIIIIJEGHG5=AEHHGFDFDDDCECEC?=@BB?ABCCCD@ -@C0HVYACXX120402:2:2105:12643:78336 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-@@@FFFFFHDHHHIJJDHIJGHGIEHIJJJGGHGIGII@HCEIIGGIJIII@FFEHGIHG@@ACEEDEBBEECEDD -@C0HVYACXX120402:2:1106:13179:108296 -CACTGTGGAATCTCGGCAGGCCCAGGACCTCGCCCGAAGCTACGGCATCCCCTACCTCGAGACCTCGGCCAAGACC -+ -@B@<;DDFHFGB+:?)CF3?:B)6@:7?:6'8)8;A8/@7;;?(,((--53;938@@BB(55<<CCABCCCDCDCCCDCC>CBDDDCCCCCBDC -@C0HVYACXX120402:2:1107:20854:145640 -GGGGCCTGGGCCTGGCTGAGCAGGGCCCTCCTTGGCAGGTGGGGCAGGAGACCCTGTAGGAGGACCCCGGGCCGCA -+ -@@CFFFDDBHHHDGFGIIGIGGJGGGIJGGGCEHIGIIF?@FBBAAGH=?@DDC@E@ECCC>B?@@ -@C0HVYACXX120402:2:1108:5651:15094 -CCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGACACTGAGTGCTGCTCCCTGGCAAG -+ -?==;;))02ACB+<3A+:AFGECHCCDDE@@(8;8;.))/BFGHHC############################## -@C0HVYACXX120402:2:1202:11055:187078 -GATGTAGGGGATGCCGTAGCTTCGGGCGAGGTCCTGAGCCTGCCGAGATTCCACAGTGCGTGCAGCCAGGTCACAC -+ -@;?ADDDFGGHDDEGI@BGHGIEFBHBG6FG7;@C@A3=C=D=?EDDA=3@CCCC=5>>?8==ACDD<8?::A>C@ -@C0HVYACXX120402:2:1204:10977:133698 -CAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAATCCTGCAGGAGGACAGGGCTCAGGGACCCCCTC -+ -@@BFDFFFHHGGHIJJIIIIJIJJGIJJJIJJJJIIJFHGJJGGCHEHJIIJIJEIIIHHHHFFEFEDCABD?=?B -@C0HVYACXX120402:2:1207:13597:158726 -ATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAATCCTGCAGGAGGACAGGG -+ -B@@DFDDFFDFFHGIGHDD=AEHBGHFIIJIEHGCDBDHGEGIJGGBGBFGGAAHGCHC7@EHGFHFFE<;ACDDB -@C0HVYACXX120402:2:1208:12152:40423 -CTCACCTGCGTCAGGAGAGCACACACTTGCAGCTCATGCAGCCGGGGCCACTCTCATCAGGAGGGTTCAGCTTCCG -+ -@@@BDFFDFDFCFFCHGBEHEHCHGIJJIEGGHAFH@GII@A@E>C@?CDEEAC:@AC?BB553>A< -@C0HVYACXX120402:2:1304:2447:13230 -GCACGCACTGTGGAATCTCGGCAGGCTCAGGACCTCGCCCGAAGCTACGGCATCCCCTACATCGAGACCTCGGCCA -+ -CCCFFFFFHHHHHIJJJJJJJJIJJEFGEFHAFFBDBDFHB@HBBEFHEDDCCCCDDC??:>@8?BDBD>@B@BB0 -@C0HVYACXX120402:2:1304:10709:146499 -CAGGCAGGGGCCTCCTGTCCTCTCTGCGCATGTCCTGGATGCCGCTGCGCCTGCAGCCCCCGTAGCCAGCTCTCGC -+ -BHGAA@FFE0DGDFDHDH@B@ -@C0HVYACXX120402:2:1304:16584:143472 -CACCTGCGTCAGGAGAGCACACACTTGCAGCTCATGCAGCCGGGGCCACTCTCATCAGGAGGGTTCAGCTTCCGCA -+ -CCCFFFFFHHHHHJGHIIGGIGGIJJJJJIIIJJIGHJIGGIJJJIHGFHDFFFFFEEEEDDD??BDDDDDDDDDD -@C0HVYACXX120402:2:1305:8052:134605 -TACTCCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGG -+ -B@@FFDEFFHHHHJHDIIIFFEGHIFGGIJIEGHIDAHGACEEBDFDDEBCEDDDCA@CCCDDDDBCCCDDDBB<@ -@C0HVYACXX120402:2:1305:13049:61181 -GCAGCTCTCCACCCCACAGCTAGCCAGGGACCCGCCCCGCCCCGCCCCAGCCAGGGAGCAGCACTCACTGACCCTC -+ -CCCFFFFFHHHHHJJJIJIJJJJJJJJIGGIJJGIJIIIIJIHDCDDDDDDDBDDBBDDDDDCDDDCDDDCDDDCB -@C0HVYACXX120402:2:1305:13225:67333 -TGTACTGGTGGATGTCCTCAAAAGACTTGGTGTTGTTGATGGCAAACACACACAGGAAGCCCTCCCCGGTGCGCAT -+ -CC@FFFFFHHHHGJIJIJJIJJHIIJIJJJFGHIJIJIGIJJJJJJJJIJIEIJIJJIJJGIJHHHFFDDDDDDDB -@C0HVYACXX120402:2:2105:6582:86372 -AGGGAGAGGCTGGCTGTGTGAACTCCCCCCACGGAAGGTCCTGAGGGGGTCCCTGAGCCCTGTCCTCCTGCAGGAT -+ -@BB<: -@C0HVYACXX120402:2:2105:12643:78336 -TCCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCTGCTTCCGGTAGGAAT -+ -CCCFFFFFHHGHDGHGGHGIIIJIEHHHHJJJIJEHIEGECHFFEFFCEECEDDDDDDDDDDDDDDDDDBB@BDDD -@C0HVYACXX120402:2:2106:18356:113683 -CGCATGGCGCTGTACTCCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCACCT -+ -@@?DDDDFFDA?FIEFHJIEHIGCEHAEGHI;BCCEHHFFFEFEA@@CAAABDBB<CBCDCCAACCDC@B@8 -@C0HVYACXX120402:2:2106:20862:32107 -TCTAGAGGAGGGGAGTCCCTCGTCTCAGCACCCCAGGAGAGGAGGGGGCATGAGGGGCATGAGAGGTACCAGGGAG -+ -@@@DFFFFBFHHFGHAEHHEHGGIGHIG>DHIIGGHGCH=CE=DGHFDD>AB@CDDDDDDDCC:@?(:CACCBB8< -@C0HVYACXX120402:2:2204:17320:181699 -ATGCCGTAGCTTCGGGCGAGGTCCTGAGCCTGCCGAGATTCCACAGTGCGTGCAGCCAGGTCACACTTGTTCCCCA -+ -CCCFFFFFHHHHHJJGGIIJIGHIJJGGEHHGIIJGGIHHHHGHHFCEEDDCBBDDBBDDDDDDDDDDD@CDDDDD -@C0HVYACXX120402:2:2206:7444:98504 -CGTAGCTTCGGGCGAGGTCCTGAGCCTGCCGAGATTCCACAGTGCGTGCAGCCAGGTCACACTTGTTCCCCACCAG -+ -?B?BD?DED<1)@@@CC:?<FGGDD6A@';=)77=7@CH@859>;>CA9@;;@>A@CC@@:@:3:5,09?A -@C0HVYACXX120402:2:2207:12031:29144 -TCCACCCCACAGCTAGCCAGGGACCCGCCCCGCCCCGCCCCAGCCAGGGAGCAGCACTCACTGACCCTCTCCCTTG -+ -CCCFFFFFGHHHHJJJJJJJJJJJJJJJJJJJJJJJFGFDDDDBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD -@C0HVYACXX120402:2:2302:11679:110301 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-@D0RE2ACXX120401:1:1102:9982:81126 -AGCCAGGTCACACTTGTTCCCCACCAGCACCATGGGCACGTCATCCGAGTCCTTCACCCGTTTGATCTGCTCCCTG -+ -B@CFFFFDHFHHHIJJGHIIJJJJIJJJJJJJJIIJIJIJEHIJJFIJJHIJJJJJIJJIEHHHFFFFFFEEEDEC -@D0RE2ACXX120401:1:1105:14437:113533 -ACAGGCCGGTCCCTCCTGATCCCATCCCTCCTTTCCCAGGGAGTGGAGGATGCCTTCTACACGTTGGTGCGTGAGA -+ -@@@DDADDFH8FFBEGGBABH<@FGIDG3?BFGFBC@?FD?707BD)@CG)=CHACHH:;BDD@;=25=:85;5?: -@D0RE2ACXX120401:1:1106:11234:42926 -TGGCCCGGGAGCCCACGCCGCACAGGTGGGGCCAGGCCGGCTGCGTCCAGGAAGGGGCCTCCTGTCCTCTCTGCGC -+ -???DDDDAHDD6CFGGDAGHAA0DDHFBCGHIHHHBB=AA'38::>CA:459 -@D0RE2ACXX120401:1:1106:17018:142120 -GCCGGCCAGGAGGAGTACAGCGCCATGCGGGACCAGTACATGCGCACCGGGGAGGGCTTCCTGTGTGTGTTTGCCA -+ -CCCFFFFFHHHHGIJEGEHJIJJIJIJJJJJIFHIJHIJJJJHHHFFDDDDD?BDDDDDDDDDDDDDBDDDDCDD> -@D0RE2ACXX120401:1:1106:18251:98846 -ATTCCTACCGGAAGCAGGTGGTCATTGATGGGGAGACGTGCCTGTTGGACATCCTGGATACCGCCGGCCAGGAGGA -+ -@C@FFFDAH:DHDGEHHEH@EB< -@D0RE2ACXX120401:1:1108:3327:3502 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-GCGTCCAGGCAGGGGCCTCCTGTCCTCTCTGCGCATGTCCTGGATGCCGCTGCGCCTGCAGCCCCCGTAGCCAGCT -+ -BBCFFFFDH8DFHHIIJIJJIIHIJJGIIJIJJJJIJHIIIJJIIJJJJJJHHFFDDCCDDDDDDDDBDDBC>BDC -@D0RE2ACXX120401:1:2107:2869:52980 -CCCGCATGGCGCTGTACTCCTCCTGGCCGGCGGTATCCAGGATGTCCAACAGGCACGTCTCCCCATCAATGACCAC -+ -@CCFFFFDFHDHDFHIIJJIIIGJJIJJJFJJGEHFFEFDC;ACEEFDCDDDDDDDDBDDDDCDDCDDCDDDDDC? -@D0RE2ACXX120401:1:2107:15207:33818 -CGTCATCCGAGTCCTTCACCCGTTTGATCTGCTCCCTGAGAGGTGGAAAGCGAGAGCTGGCTACGGGGGCTGCAGG -+ -@@@DFFFFHDDHHIJGHGIIGGFGGAGHIIGIIJIJJJDEFHI0?BFGIGIJIFHHGEFFHCADEFCDBD;BBDDB -@D0RE2ACXX120401:1:2202:19767:187606 -GTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGGCCCCGGCGAGGTGTGGGGGGGAGAGCTTCCTCC -+ -@@@DDB;DDHDFDADGBDHGGI@AFGCGEEBHB60:B####################################### -@D0RE2ACXX120401:1:2204:15074:94989 -GTGGTGGTGGGCGCCGGCGGTGTGGGCAAGAGTGCGCTGACCATCCAGCTGATCCAGAACCACTTTGTGGACGAAT -+ -@@CFDDF@FHHGHIIIIIII6BAEHHFFFFEE;ACBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCDCDDDD8 -@D0RE2ACXX120401:1:2204:17021:168013 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6cce286..0000000 --- a/tests/data/D0RH0.2_r2.fq +++ /dev/null @@ -1,100 +0,0 @@ -@D0RH0ACXX120402:2:1101:9941:91233 -GAGCAGATCAAACGGGTGAAGGACTCGGATGACGTGCCCATGGTGCTGGTGGGGAACAAGTGTGACCTGGCTGCAC -+ -@C@DDDDDFHHHHIIIFEHHHHGHCHIJIEBFDHGHGIJGGII8CGHCG=8;EH?DFFFC>>;ACEC>(;ACBDDC -@D0RH0ACXX120402:2:1104:15433:66813 -TGGGGTCGTATTCGTCCACAAAGTGGTTCTGGATCAGCTGGATGGTCAGCGCACTCTTGCCCACACCGCCGGCGCC -+ -BCCFFDFFHFHHHJBHIJJICF>:EGEGGGIJJIJGGJJIJIJIJDFIGIHIIJIHHHHHFFFFFDDDDDDDDDDB -@D0RH0ACXX120402:2:1109:5317:15000 -ATCCAGCTGATCCAGAACCACTTTGTGGACGAATACGACCCCACTATAGAGGTGAGCCTGGCGCCGCCGTCCAGGT -+ -C@CFFFFFHGHHHJJJGJJJJJJJJGIJJJIJIJJIIJJJIJJJJJJJJJHI=DHIIHHHHFFDDDDDD@BDDDDD -@D0RH0ACXX120402:2:1113:17636:96710 -GCAGCTCTCCACCCCACAGCTAGCCAGGGACCCGCCCCGCCCCGCCCCAGCCAGGGAGCAGCACTCACTGACCCTC -+ -CCCFFFFFHHHHHJJIGIIGIIIFIIJJJIJIIFEIJJGIJJHFDDDDDDBBDDDDBBBBDDDDDDDDDDDDDDDB -@D0RH0ACXX120402:2:1114:9843:34912 -GCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCGGGTCTTGGCCGAGGTCTCGATGTAGGGGATGCCGTAGCTTC -+ 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indexfilename=HCC1143_BAM_INPUT.3.20190812.wgs.grch38.bam.bai index=1 I=/var/lib/cwl/stg8660adc5-93d6-4599-897d-94a85572c97f/grch38-aligned.C0HVY_2.lane.bam I=/var/lib/cwl/stg03d360cd-eb6a-4a47-bac6-43c95f903501/grch38-aligned.D0RE2_1.lane.bam I=/var/lib/cwl/stgb19de994-8820-4d05-aa3f-3bacc809e6db/grch38-aligned.D0RH0_2.lane.bam - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -Pond-147580 0 84 2 0 3 0 0.0357143 1147 - -## HISTOGRAM -BIN VALUE -1 0.999974 -2 1.92933 -3 2.79306 -4 3.5958 -5 4.34185 -6 5.03521 -7 5.67961 -8 6.27851 -9 6.83511 -10 7.35241 -11 7.83318 -12 8.27999 -13 8.69526 -14 9.0812 -15 9.43988 -16 9.77324 -17 10.0831 -18 10.371 -19 10.6386 -20 10.8873 -21 11.1184 -22 11.3333 -23 11.5329 -24 11.7185 -25 11.8909 -26 12.0512 -27 12.2001 -28 12.3386 -29 12.4672 -30 12.5868 -31 12.6979 -32 12.8012 -33 12.8972 -34 12.9864 -35 13.0693 -36 13.1464 -37 13.218 -38 13.2846 -39 13.3464 -40 13.4039 -41 13.4573 -42 13.507 -43 13.5531 -44 13.596 -45 13.6359 -46 13.6729 -47 13.7074 -48 13.7394 -49 13.7691 -50 13.7967 -51 13.8224 -52 13.8463 -53 13.8685 -54 13.8891 -55 13.9083 -56 13.9261 -57 13.9426 -58 13.958 -59 13.9723 -60 13.9856 -61 13.998 -62 14.0094 -63 14.0201 -64 14.03 -65 14.0392 -66 14.0478 -67 14.0558 -68 14.0631 -69 14.07 -70 14.0764 -71 14.0823 -72 14.0879 -73 14.093 -74 14.0978 -75 14.1022 -76 14.1063 -77 14.1101 -78 14.1137 -79 14.117 -80 14.1201 -81 14.1229 -82 14.1256 -83 14.128 -84 14.1303 -85 14.1325 -86 14.1344 -87 14.1363 -88 14.138 -89 14.1396 -90 14.1411 -91 14.1424 -92 14.1437 -93 14.1449 -94 14.146 -95 14.147 -96 14.148 -97 14.1489 -98 14.1497 -99 14.1504 -100 14.1511 diff --git a/tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam b/tests/data/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam deleted file mode 100644 index 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I=/var/lib/cwl/stgbcba7c01-3201-4a9c-be26-6f07e886550c/grch38-aligned.C0HVY_2.lane.bam I=/var/lib/cwl/stg4d9808b8-e57b-47a3-a1a0-9e775ea8089a/grch38-aligned.D0RE2_1.lane.bam I=/var/lib/cwl/stga817a9d4-8336-4e44-ad8f-e152c8fbb453/grch38-aligned.D0RH0_2.lane.bam - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -Pond-147580 0 84 2 0 3 0 0.0357143 1147 - -## HISTOGRAM -BIN VALUE -1 0.999974 -2 1.92933 -3 2.79306 -4 3.5958 -5 4.34185 -6 5.03521 -7 5.67961 -8 6.27851 -9 6.83511 -10 7.35241 -11 7.83318 -12 8.27999 -13 8.69526 -14 9.0812 -15 9.43988 -16 9.77324 -17 10.0831 -18 10.371 -19 10.6386 -20 10.8873 -21 11.1184 -22 11.3333 -23 11.5329 -24 11.7185 -25 11.8909 -26 12.0512 -27 12.2001 -28 12.3386 -29 12.4672 -30 12.5868 -31 12.6979 -32 12.8012 -33 12.8972 -34 12.9864 -35 13.0693 -36 13.1464 -37 13.218 -38 13.2846 -39 13.3464 -40 13.4039 -41 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a/tests/data/broad-mutect2.snv-indel.vcf.gz b/tests/data/broad-mutect2.snv-indel.vcf.gz deleted file mode 100644 index e69de29..0000000 diff --git a/tests/data/broad-mutect2.snv-indel.vcf.gz.tbi b/tests/data/broad-mutect2.snv-indel.vcf.gz.tbi deleted file mode 100644 index e69de29..0000000 diff --git a/tests/data/dna_alignment.test.json b/tests/data/dna_alignment.test.json deleted file mode 100644 index 5a0329d..0000000 --- a/tests/data/dna_alignment.test.json +++ /dev/null @@ -1,103 +0,0 @@ -{ - "type": "dna_alignment", - "program_id": "TEST-PRO", - "id": "23a74103-1a9d-4bf3-8e06-0e8c33e8419e", - "inputs": { - "reference_genome": { - }, - "lane_seq": [ - { - "lane_seq_submission_id": "c3ec531b-c2c9-4c77-894a-5b80dd18241e", - "files": { - "lane_seq": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "C0HVY_2.lane.bam", - "path": "/var/lib/cwl/stgf12233dd-cace-4fea-8918-53312f96ce4d/C0HVY_2.lane.bam", - "size": 4018, - "checksum": "8d0070078bd2a5695225bbf42a0f85d1", - "checksum_type": "md5", - "object_id": "0ee0d7f2-e96c-4e8c-be55-91267e74670b", - "bundle_id": "c3ec531b-c2c9-4c77-894a-5b80dd18241e" - } - } - }, - { - "lane_seq_submission_id": "02adbffc-c6f1-49d0-9518-e2d6d0c86f33", - "files": { - "lane_seq": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "D0RE2_1.lane.bam", - "path": "/var/lib/cwl/stgcdf099fa-26d7-414c-9287-b786a4eb2bb9/D0RE2_1.lane.bam", - "size": 4600, - "checksum": "e6800701dda4aebc0f34a248a10a547d", - "checksum_type": "md5", - "object_id": "4032dea0-60ec-4094-8805-16723de70e3f", - "bundle_id": "02adbffc-c6f1-49d0-9518-e2d6d0c86f33" - } - } - }, - { - "lane_seq_submission_id": "a64548d3-9ed9-4ad4-913e-0b7b94658265", - "files": { - "lane_seq": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "D0RH0_2.lane.bam", - "path": "/var/lib/cwl/stga0fb59a5-6a99-4fc3-8208-1e84c8604e92/D0RH0_2.lane.bam", - "size": 3705, - "checksum": "4a45a72a66b3e21f0c5e37b941c5e134", - "checksum_type": "md5", - "object_id": "ffcd79d6-a7fb-47ba-81d9-f9cd2a63c84f", - "bundle_id": "a64548d3-9ed9-4ad4-913e-0b7b94658265" - } - } - } - ] - }, - "analysis": { - "analysis_type": "DNA alignment", - "reference_genome": "GRCh38", - "tool": { - "id": "87450266-33b5-45ea-97c6-6e621498b066", - "name": "dna_alignment", - "version": "0.1.0", - "included_apps": [ - "bwa mem", - "samtools", - "biobambam" - ] - }, - "execution": { - "runner_name": "cwltool", - "runner_version": "1.0.20190618201008", - "job_id": "1427c458-6954-46ca-a780-a9fe5ccdd62f", - "started_at": "2019-07-05T08:15:30+00:00", - "completed_at": "2019-07-05T08:15:30+00:00" - } - }, - "files": { - "aligned_seq": { - "type": "dna_alignment.aligned_seq.data_object", - "name": "HCC1143.3.20190726.wgs.grch38.bam", - "path": "/var/lib/cwl/stg2fd25978-132b-4c01-bb47-2809eb78da2a/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam", - "size": 13198, - "checksum": "9f8bd59e0ab446bb01a367689cbb0467", - "checksum_type": "md5", - "object_id": "e2fccb90-9eac-4664-9dd2-f2517bba1bdb" - }, - "aligned_seq_index": { - "type": "dna_alignment.aligned_seq_index.data_object", - "name": "HCC1143.3.20190726.wgs.grch38.bam.bai", - "path": "/var/lib/cwl/stg2fd25978-132b-4c01-bb47-2809eb78da2a/HCC1143_BAM_INPUT.3.20190814.wgs.grch38.bam.bai", - "size": 352, - "checksum": "c532221edfc6bed662cf944e1aa887ac", - "checksum_type": "md5", - "object_id": "79c196c7-62c8-44d7-ba8d-2c1980046ac3" - } - }, - "info": { - "library_strategy": "WGS", - "submitter_sample_id": "HCC1143_BAM_INPUT", - "submitter_donor_id": "HCC1143", - "tumour_normal_designation": "Cell line - derived from tumour" - } -} diff --git a/tests/data/experiment-fq.tsv b/tests/data/experiment-fq.tsv deleted file mode 100644 index 0964718..0000000 --- a/tests/data/experiment-fq.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id tumour_normal_designation submitter_sample_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count gender submitter_specimen_id -sequencing_experiment TEST-PRO TEST_EXP HCC1143 Cell line - derived from tumour HCC1143_FASTQ_INPUT EXT Illumina HiSeq 2000 WGS 2014-12-12 3 female HCC1143_FASTQ_INPUT diff --git a/tests/data/experiment-fq.v2.fake-PACA-CA.tsv b/tests/data/experiment-fq.v2.fake-PACA-CA.tsv deleted file mode 100644 index 7ac0b17..0000000 --- a/tests/data/experiment-fq.v2.fake-PACA-CA.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count -sequencing_experiment PACA-CA TEST_EXP PCSI_0216 Male PCSI_0216_Pa_P_526 Tumour Primary tumour Blood derived PCSI_0216_Pa_P_526 Total DNA PCSI_0216_St_R EXT ILLUMINA HiSeq 2000 WGS 2014-12-12 3 diff --git a/tests/data/experiment-fq.v2.tsv b/tests/data/experiment-fq.v2.tsv deleted file mode 100644 index 8ea12f0..0000000 --- a/tests/data/experiment-fq.v2.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count -sequencing_experiment TEST-PR TEST_EXP1 HCC1143 Female HCC1143_BAM_INPUT Normal Normal Blood derived HCC1143_BAM_INPUT Total DNA EXT ILLUMINA HiSeq 2000 WGS 2014-12-12 3 diff --git a/tests/data/experiment-lgc-bam.v2.tsv b/tests/data/experiment-lgc-bam.v2.tsv deleted file mode 100644 index 6cbae9f..0000000 --- a/tests/data/experiment-lgc-bam.v2.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count -sequencing_experiment TEST-PR EGAR00001229200 HCC1143 Female HCC1143_BAM_INPUT Normal Normal Blood derived HCC1143_BAM_INPUT Total DNA OICR ILLUMINA HiSeq 2000 WXS 2014-12-12 1 diff --git a/tests/data/experiment.tsv b/tests/data/experiment.tsv deleted file mode 100644 index f087830..0000000 --- a/tests/data/experiment.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id gender tumour_normal_designation submitter_sample_id submitter_specimen_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count -sequencing_experiment TEST-PRO TEST_EXP HCC1143 female Normal - EBV immortalized HCC1143_BAM_INPUT HCC1143_BAM_INPUT EXT Illumina HiSeq 2000 WGS 2014-12-12 3 diff --git a/tests/data/experiment.v2.fake-PACA-CA.tsv b/tests/data/experiment.v2.fake-PACA-CA.tsv deleted file mode 100644 index 65bcae3..0000000 --- a/tests/data/experiment.v2.fake-PACA-CA.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count -sequencing_experiment PACA-CA TEST_EXP PCSI_0216 Male PCSI_0216_St_R Normal Normal Solid tissue PCSI_0216_St_R Total DNA ILLUMINA HiSeq 2000 WGS 2014-12-12 3 diff --git a/tests/data/experiment.v2.tsv b/tests/data/experiment.v2.tsv deleted file mode 100644 index c92c78d..0000000 --- a/tests/data/experiment.v2.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type program_id submitter_sequencing_experiment_id submitter_donor_id gender submitter_specimen_id tumour_normal_designation specimen_type specimen_tissue_source submitter_sample_id sample_type submitter_matched_normal_sample_id sequencing_center platform platform_model library_strategy sequencing_date read_group_count -sequencing_experiment TEST-PR TEST_EXP HCC1143 Female HCC1143_BAM_INPUT Normal Normal Blood derived HCC1143_BAM_INPUT Total DNA EXT ILLUMINA HiSeq 2000 WGS 2014-12-12 3 diff --git a/tests/data/file-fq.tsv b/tests/data/file-fq.tsv deleted file mode 100644 index d7d4450..0000000 --- a/tests/data/file-fq.tsv +++ /dev/null @@ -1,7 +0,0 @@ -type name size submitter_read_group_id checksum checksum_type path format -file C0HVY.2_r1.fq 5381 C0HVY.2 6584ebb05edfbd6f59be6307556bd871 md5 C0HVY.2_r1.fq FASTQ -file C0HVY.2_r2.fq 5381 C0HVY.2 d649696f346eb75b95b68e8ecd45f44f md5 C0HVY.2_r2.fq FASTQ -file D0RE2.1_r1.fq 6148 D0RE2.1 058510bbdab2dccc14a2d7402a21248d md5 D0RE2.1_r1.fq FASTQ -file D0RE2.1_r2.fq 6148 D0RE2.1 5fb35647198666b6a06e8539074282fd md5 D0RE2.1_r2.fq FASTQ -file D0RH0.2_r1.fq 4784 D0RH0.2 eb109b8774df03084024bc09a86721be md5 D0RH0.2_r1.fq FASTQ -file D0RH0.2_r2.fq 4784 D0RH0.2 ed209fda15a5928087104253a6bfb42d md5 D0RH0.2_r2.fq FASTQ \ No newline at end of file diff --git a/tests/data/file-fq.v2.tsv b/tests/data/file-fq.v2.tsv deleted file mode 100644 index bd3ee0c..0000000 --- a/tests/data/file-fq.v2.tsv +++ /dev/null @@ -1,7 +0,0 @@ -type name format size md5sum path -file C0HVY.2_r1.fq FASTQ 5381 6584ebb05edfbd6f59be6307556bd871 C0HVY.2_r1.fq -file C0HVY.2_r2.fq FASTQ 5381 d649696f346eb75b95b68e8ecd45f44f C0HVY.2_r2.fq -file D0RE2.1_r1.fq FASTQ 6148 058510bbdab2dccc14a2d7402a21248d D0RE2.1_r1.fq -file D0RE2.1_r2.fq FASTQ 6148 5fb35647198666b6a06e8539074282fd D0RE2.1_r2.fq -file D0RH0.2_r1.fq FASTQ 4784 eb109b8774df03084024bc09a86721be D0RH0.2_r1.fq -file D0RH0.2_r2.fq FASTQ 4784 ed209fda15a5928087104253a6bfb42d D0RH0.2_r2.fq diff --git a/tests/data/file-lgc-bam.v2.tsv b/tests/data/file-lgc-bam.v2.tsv deleted file mode 100644 index 3de4539..0000000 --- a/tests/data/file-lgc-bam.v2.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type name format size md5sum path -file 48567b015eb396800bd218096c0fc12c.PCSI_0056_St_R_PE_363_EX_NoIndex_6_110513_I580_00041_70GG8_JJ.bam BAM 282154769 48567b015eb396800bd218096c0fc12c score://collab/EGAR00001229200/e07e1694-162a-59ff-b5de-0d51e32461cf diff --git a/tests/data/file.tsv b/tests/data/file.tsv deleted file mode 100644 index b89c426..0000000 --- a/tests/data/file.tsv +++ /dev/null @@ -1,4 +0,0 @@ -type name size submitter_read_group_id checksum checksum_type path format -file test_rg_3.bam 14899 C0HVY.2 247581f6d2324ee3860158334fe517c8 md5 test_rg_3.bam BAM -file test_rg_3.bam 14899 D0RE2.1 247581f6d2324ee3860158334fe517c8 md5 test_rg_3.bam BAM -file test_rg_3.bam 14899 D0RH0.2 247581f6d2324ee3860158334fe517c8 md5 test_rg_3.bam BAM \ No newline at end of file diff --git a/tests/data/file.v2.tsv b/tests/data/file.v2.tsv deleted file mode 100644 index e666186..0000000 --- a/tests/data/file.v2.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type name format size md5sum path -file test_rg_3.v2.bam BAM 14911 178f97f7b1ca8bfc28fd5586bdd56799 test_rg_3.v2.bam diff --git a/tests/data/lane_seq_submission.C0HVY_2.json b/tests/data/lane_seq_submission.C0HVY_2.json deleted file mode 100644 index 11b394e..0000000 --- a/tests/data/lane_seq_submission.C0HVY_2.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "type": "lane_seq_submission", - "program_id": "TEST-PRO", - "id": "c3ec531b-c2c9-4c77-894a-5b80dd18241e", - "inputs": { - "submitter_read_group_id": "C0HVY.2", - "files": { - "bam": { - "name": "test_rg_3.bam", - "size": 133684363564, - "submitter_read_group_id": [ - "C0HVY.2", - "D0RH0.2", - "D0RE2.1" - ], - "checksum": "e4fe8353ae62045642a2124909c5cfa5", - "checksum_type": "md5", - "path": "score://collaboratory/EGAZ00001018588/7aba9867-ffba-5e57-96d0-300c80839504", - "format": "BAM", - "type": "sequencing_file" - } - } - }, - "files": { - "bam_file": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "C0HVY_2.lane.bam", - "path": "/var/lib/cwl/stgf12233dd-cace-4fea-8918-53312f96ce4d/C0HVY_2.lane.bam", - "size": 4018, - "checksum": "8d0070078bd2a5695225bbf42a0f85d1", - "checksum_type": "md5", - "object_id": "0ee0d7f2-e96c-4e8c-be55-91267e74670b" - } - }, - "info": { - "library_strategy": "WGS", - "submitter_sample_id": "HCC1143_BAM_INPUT", - "submitter_donor_id": "HCC1143", - "tumour_normal_designation": "Cell line - derived from tumour" - } -} diff --git a/tests/data/lane_seq_submission.C0HVY_2.lane.bam.json b/tests/data/lane_seq_submission.C0HVY_2.lane.bam.json deleted file mode 100644 index db02c78..0000000 --- a/tests/data/lane_seq_submission.C0HVY_2.lane.bam.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "type": "lane_seq_submission", - "program_id": "TEST-PRO", - "id": "c3ec531b-c2c9-4c77-894a-5b80dd18241e", - "inputs": { - "submitter_read_group_id": "C0HVY.2", - "files": { - "bam": { - "name": "test_rg_3.bam", - "size": 133684363564, - "submitter_read_group_id": [ - "C0HVY.2", - "D0RH0.2", - "D0RE2.1" - ], - "checksum": "e4fe8353ae62045642a2124909c5cfa5", - "checksum_type": "md5", - "path": "score://collaboratory/EGAZ00001018588/7aba9867-ffba-5e57-96d0-300c80839504", - "format": "BAM", - "type": "sequencing_file" - } - } - }, - "files": { - "bam_file": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "C0HVY_2.lane.bam", - "path": "/var/lib/cwl/stgf12233dd-cace-4fea-8918-53312f96ce4d/C0HVY_2.lane.bam", - "size": 4018, - "checksum": "8d0070078bd2a5695225bbf42a0f85d1", - "checksum_type": "md5", - "object_id": "0ee0d7f2-e96c-4e8c-be55-91267e74670b" - } - } - } \ No newline at end of file diff --git a/tests/data/lane_seq_submission.D0RE2_1.json b/tests/data/lane_seq_submission.D0RE2_1.json deleted file mode 100644 index a26e304..0000000 --- a/tests/data/lane_seq_submission.D0RE2_1.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "type": "lane_seq_submission", - "program_id": "TEST-PRO", - "id": "c3ec531b-c2c9-4c77-894a-5b80dd18241e", - "inputs": { - "submitter_read_group_id": "D0RE2.1", - "files": { - "bam": { - "name": "test_rg_3.bam", - "size": 133684363564, - "submitter_read_group_id": [ - "C0HVY.2", - "D0RH0.2", - "D0RE2.1" - ], - "checksum": "e4fe8353ae62045642a2124909c5cfa5", - "checksum_type": "md5", - "path": "score://collaboratory/EGAZ00001018588/7aba9867-ffba-5e57-96d0-300c80839504", - "format": "BAM", - "type": "sequencing_file" - } - } - }, - "files": { - "bam_file": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "D0RE2_1.lane.bam", - "path": "/var/lib/cwl/stgf12233dd-cace-4fea-8918-53312f96ce4d/D0RE2_1.lane.bam", - "size": 4551, - "checksum": "8d0070078bd2a5695225bbf42a0f85d1", - "checksum_type": "md5", - "object_id": "0ee0d7f2-e96c-4e8c-be55-91267e74670b" - } - }, - "info": { - "library_strategy": "WGS", - "submitter_sample_id": "HCC1143_BAM_INPUT", - "submitter_donor_id": "HCC1143", - "tumour_normal_designation": "Cell line - derived from tumour" - } -} diff --git a/tests/data/lane_seq_submission.D0RE2_1.lane.bam.json b/tests/data/lane_seq_submission.D0RE2_1.lane.bam.json deleted file mode 100644 index 52b1166..0000000 --- a/tests/data/lane_seq_submission.D0RE2_1.lane.bam.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "type": "lane_seq_submission", - "program_id": "TEST-PRO", - "id": "02adbffc-c6f1-49d0-9518-e2d6d0c86f33", - "inputs": { - "submitter_read_group_id": "D0RE2.1", - "files": { - "bam": { - "name": "test_rg_3.bam", - "size": 133684363564, - "submitter_read_group_id": [ - "C0HVY.2", - "D0RH0.2", - "D0RE2.1" - ], - "checksum": "e4fe8353ae62045642a2124909c5cfa5", - "checksum_type": "md5", - "path": "score://collaboratory/EGAZ00001018588/7aba9867-ffba-5e57-96d0-300c80839504", - "format": "BAM", - "type": "sequencing_file" - } - } - }, - "files": { - "bam_file": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "D0RE2_1.lane.bam", - "path": "/var/lib/cwl/stgcdf099fa-26d7-414c-9287-b786a4eb2bb9/D0RE2_1.lane.bam", - "size": 4600, - "checksum": "e6800701dda4aebc0f34a248a10a547d", - "checksum_type": "md5", - "object_id": "4032dea0-60ec-4094-8805-16723de70e3f" - } - } - } \ No newline at end of file diff --git a/tests/data/lane_seq_submission.D0RH0_2.lane.bam.json b/tests/data/lane_seq_submission.D0RH0_2.lane.bam.json deleted file mode 100644 index e56fa4e..0000000 --- a/tests/data/lane_seq_submission.D0RH0_2.lane.bam.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "type": "lane_seq_submission", - "program_id": "TEST-PRO", - "id": "a64548d3-9ed9-4ad4-913e-0b7b94658265", - "inputs": { - "submitter_read_group_id": "D0RH0.2", - "files": { - "bam": { - "name": "test_rg_3.bam", - "size": 133684363564, - "submitter_read_group_id": [ - "C0HVY.2", - "D0RH0.2", - "D0RE2.1" - ], - "checksum": "e4fe8353ae62045642a2124909c5cfa5", - "checksum_type": "md5", - "path": "score://collaboratory/EGAZ00001018588/7aba9867-ffba-5e57-96d0-300c80839504", - "format": "BAM", - "type": "sequencing_file" - } - } - }, - "files": { - "bam_file": { - "type": "lane_seq_submission.bam_file.data_object", - "name": "D0RH0_2.lane.bam", - "path": "/var/lib/cwl/stga0fb59a5-6a99-4fc3-8208-1e84c8604e92/D0RH0_2.lane.bam", - "size": 3705, - "checksum": "4a45a72a66b3e21f0c5e37b941c5e134", - "checksum_type": "md5", - "object_id": "ffcd79d6-a7fb-47ba-81d9-f9cd2a63c84f" - } - } - } \ No newline at end of file diff --git a/tests/data/read_group-fq.tsv b/tests/data/read_group-fq.tsv deleted file mode 100644 index fce8798..0000000 --- a/tests/data/read_group-fq.tsv +++ /dev/null @@ -1,4 +0,0 @@ -type submitter_read_group_id platform_unit is_paired_end read_length_r1 read_length_r2 insert_size sample_barcode library_name submitter_sequencing_experiment_id -read_group C0HVY.2 74_8 True 150 150 298 Pond-147580 TEST_EXP -read_group D0RE2.1 74_8 True 150 150 298 Pond-147580 TEST_EXP -read_group D0RH0.2 74_8 True 150 150 298 Pond-147580 TEST_EXP diff --git a/tests/data/read_group-fq.v2.tsv b/tests/data/read_group-fq.v2.tsv deleted file mode 100644 index bc0944e..0000000 --- a/tests/data/read_group-fq.v2.tsv +++ /dev/null @@ -1,4 +0,0 @@ -type submitter_read_group_id submitter_sequencing_experiment_id platform_unit is_paired_end file_r1 file_r2 read_length_r1 read_length_r2 insert_size sample_barcode library_name -read_group C0HVY.2 TEST_EXP1 74_8a true C0HVY.2_r1.fq C0HVY.2_r2.fq 150 150 298 Pond-147580 -read_group D0RE2.1 TEST_EXP1 74_8b true D0RE2.1_r1.fq D0RE2.1_r2.fq 150 150 298 Pond-147580 -read_group D0RH0.2 TEST_EXP1 74_8c true D0RH0.2_r1.fq D0RH0.2_r2.fq 150 150 298 Pond-147580 diff --git a/tests/data/read_group-lgc-bam.v2.tsv b/tests/data/read_group-lgc-bam.v2.tsv deleted file mode 100644 index c503937..0000000 --- a/tests/data/read_group-lgc-bam.v2.tsv +++ /dev/null @@ -1,2 +0,0 @@ -type submitter_read_group_id submitter_sequencing_experiment_id platform_unit is_paired_end file_r1 file_r2 read_length_r1 read_length_r2 insert_size sample_barcode library_name -read_group 110513_I580_00041_70GG8_JJ_6_NoIndex EGAR00001229200 I580 true 48567b015eb396800bd218096c0fc12c.PCSI_0056_St_R_PE_363_EX_NoIndex_6_110513_I580_00041_70GG8_JJ.bam 48567b015eb396800bd218096c0fc12c.PCSI_0056_St_R_PE_363_EX_NoIndex_6_110513_I580_00041_70GG8_JJ.bam 101 101 300 PCSI_0056_St_R_PE_363_EX diff --git a/tests/data/read_group.tsv b/tests/data/read_group.tsv deleted file mode 100644 index fce8798..0000000 --- a/tests/data/read_group.tsv +++ /dev/null @@ -1,4 +0,0 @@ -type submitter_read_group_id platform_unit is_paired_end read_length_r1 read_length_r2 insert_size sample_barcode library_name submitter_sequencing_experiment_id -read_group C0HVY.2 74_8 True 150 150 298 Pond-147580 TEST_EXP -read_group D0RE2.1 74_8 True 150 150 298 Pond-147580 TEST_EXP -read_group D0RH0.2 74_8 True 150 150 298 Pond-147580 TEST_EXP diff --git a/tests/data/read_group.v2.tsv b/tests/data/read_group.v2.tsv deleted file mode 100644 index 10c2384..0000000 --- a/tests/data/read_group.v2.tsv +++ /dev/null @@ -1,4 +0,0 @@ -type submitter_read_group_id submitter_sequencing_experiment_id platform_unit is_paired_end file_r1 file_r2 read_length_r1 read_length_r2 insert_size sample_barcode library_name -read_group C0HVY.2 TEST_EXP 74_8a true test_rg_3.v2.bam test_rg_3.v2.bam 150 150 298 Pond-147580 -read_group D0RE2.1 TEST_EXP 74_8b true test_rg_3.v2.bam test_rg_3.v2.bam 150 150 298 Pond-147580 -read_group D0RH0.2 TEST_EXP 74_8c true test_rg_3.v2.bam test_rg_3.v2.bam 150 150 298 Pond-147580 diff --git a/tests/data/rg_ubam.song-analysis.01.json b/tests/data/rg_ubam.song-analysis.01.json deleted file mode 100644 index 4fa8ed7..0000000 --- a/tests/data/rg_ubam.song-analysis.01.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "analysisId": "14159e56-0159-475b-959e-560159c75b85", - "study": "TEST-PRO", - "analysisState": "UNPUBLISHED", - "sample": [ - { - "info": {}, - "sampleId": "2648e53f-cb71-5eaf-b7ec-6b4766d50e2a", - "specimenId": "2648e53f-cb71-5eaf-b7ec-6b4766d50e2a", - "sampleSubmitterId": "HCC1143_FASTQ_INPUT", - "sampleType": "DNA", - "specimen": { - "info": {}, - "specimenId": "2648e53f-cb71-5eaf-b7ec-6b4766d50e2a", - "donorId": "96c05977-b40e-5c00-8bc6-3aaa8fbdda35", - "specimenSubmitterId": "HCC1143_FASTQ_INPUT", - "specimenClass": "Tumour", - "specimenType": "Primary tumour - solid tissue" - }, - "donor": { - "donorId": "96c05977-b40e-5c00-8bc6-3aaa8fbdda35", - "donorSubmitterId": "HCC1143", - "studyId": "TEST-PRO", - "donorGender": "female", - "info": {} - } - } - ], - "file": [ - { - "info": { - "data_type": "Read Group Unmapped BAM" - }, - "objectId": "2eebd492-07d3-5903-9536-c77c57659751", - "studyId": "TEST-PRO", - "analysisId": "14159e56-0159-475b-959e-560159c75b85", - "fileName": "D0RE2_1.lane.bam", - "fileSize": 4551, - "fileType": "BAM", - "fileMd5sum": "d57f7e84fca26d288ed81eb9dfff5fe7", - "fileAccess": "controlled" - } - ], - "analysisType": { - "name": "read_group_ubam", - "version": 2 - }, - "inputs": [ - { - "sequencing_experiment_id": "a29e3ec5-b1b6-4643-9e3e-c5b1b636430e" - } - ], - "workflow": { - "name": "dna-seq-alignment", - "version": "0.2.3.0", - "short_name": "dna-seq-alignment" - }, - "experiment": {}, - "program_id": "TEST-PRO", - "insert_size": 298, - "library_name": "Pond-147580", - "is_paired_end": true, - "platform_unit": "74_8", - "read_length_r1": 150, - "read_length_r2": 150, - "sample_barcode": null, - "submitter_read_group_id": "D0RE2.1" -} diff --git a/tests/data/rg_ubam.song-analysis.02.json b/tests/data/rg_ubam.song-analysis.02.json deleted file mode 100644 index abf9e4f..0000000 --- a/tests/data/rg_ubam.song-analysis.02.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "analysisId": "5e3e5380-4c90-4901-be53-804c90f9018b", - "study": "TEST-PRO", - "analysisState": "UNPUBLISHED", - "sample": [ - { - "info": {}, - "sampleId": "SAbc064f25adab65a4c75a539e5e2b8d48", - "specimenId": "SPea740f45bacdf68583eeb9183e8bb57a", - "sampleSubmitterId": "HCC1143_BAM_INPUT", - "sampleType": "DNA", - "specimen": { - "info": {}, - "specimenId": "SPea740f45bacdf68583eeb9183e8bb57a", - "donorId": "DO1d5c9010f8ddcc4b7be855ddaa9cdd3c", - "specimenSubmitterId": "TEST_EXP", - "specimenClass": "Tumour", - "specimenType": "Primary tumour - other" - }, - "donor": { - "donorId": "DO1d5c9010f8ddcc4b7be855ddaa9cdd3c", - "donorSubmitterId": "internal_donor_123456789-00", - "studyId": "TEST-PRO", - "donorGender": "female", - "info": {} - } - } - ], - "file": [ - { - "info": { - "data_type": "Read Group Unmapped BAM" - }, - "objectId": "b5c2f9a0-b321-518d-b80d-3070aa1d6840", - "studyId": "TEST-PRO", - "analysisId": "5e3e5380-4c90-4901-be53-804c90f9018b", - "fileName": "C0HVY_2.lane.bam", - "fileSize": 3990, - "fileType": "BAM", - "fileMd5sum": "2a20e32f077348d97b3cf6c6cb4745c0", - "fileAccess": "controlled" - } - ], - "analysisType": { - "name": "read_group_ubam", - "version": 2 - }, - "inputs": [ - { - "sequencing_experiment_id": "0bbd6e1b-f38b-451c-bd6e-1bf38b451caa" - } - ], - "workflow": { - "name": "dna-seq-alignment", - "version": "0.2.3.0", - "short_name": "dna-seq-alignment" - }, - "experiment": {}, - "program_id": "TEST-PRO", - "insert_size": 298, - "library_name": "Pond-147580", - "is_paired_end": true, - "platform_unit": "74_8", - "read_length_r1": 150, - "read_length_r2": 150, - "sample_barcode": null, - "submitter_read_group_id": "C0HVY.2" -} diff --git a/tests/data/rg_ubam.song-analysis.03.json b/tests/data/rg_ubam.song-analysis.03.json deleted file mode 100644 index ae47662..0000000 --- a/tests/data/rg_ubam.song-analysis.03.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "analysisId": "83e352d7-afec-4bcc-a352-d7afecebccce", - "study": "TEST-PRO", - "analysisState": "UNPUBLISHED", - "sample": [ - { - "info": {}, - "sampleId": "2648e53f-cb71-5eaf-b7ec-6b4766d50e2a", - "specimenId": "2648e53f-cb71-5eaf-b7ec-6b4766d50e2a", - "sampleSubmitterId": "HCC1143_FASTQ_INPUT", - "sampleType": "DNA", - "specimen": { - "info": {}, - "specimenId": "2648e53f-cb71-5eaf-b7ec-6b4766d50e2a", - "donorId": "96c05977-b40e-5c00-8bc6-3aaa8fbdda35", - "specimenSubmitterId": "HCC1143_FASTQ_INPUT", - "specimenClass": "Tumour", - "specimenType": "Primary tumour - solid tissue" - }, - "donor": { - "donorId": "96c05977-b40e-5c00-8bc6-3aaa8fbdda35", - "donorSubmitterId": "HCC1143", - "studyId": "TEST-PRO", - "donorGender": "female", - "info": {} - } - } - ], - "file": [ - { - "info": { - "data_type": "Read Group Unmapped BAM" - }, - "objectId": "9fb19dbc-ed5b-5371-b39f-4d3f114c9da5", - "studyId": "TEST-PRO", - "analysisId": "83e352d7-afec-4bcc-a352-d7afecebccce", - "fileName": "D0RH0_2.lane.bam", - "fileSize": 4551, - "fileType": "BAM", - "fileMd5sum": "d57f7e84fca26d288ed81eb9dfff5fe7", - "fileAccess": "controlled" - } - ], - "analysisType": { - "name": "read_group_ubam", - "version": 2 - }, - "inputs": [ - { - "sequencing_experiment_id": "a29e3ec5-b1b6-4643-9e3e-c5b1b636430e" - } - ], - "workflow": { - "name": "dna-seq-alignment", - "version": "0.2.3.0", - "short_name": "dna-seq-alignment" - }, - "experiment": {}, - "program_id": "TEST-PRO", - "insert_size": 298, - "library_name": "Pond-147580", - "is_paired_end": true, - "platform_unit": "74_8", - "read_length_r1": 150, - "read_length_r2": 150, - "sample_barcode": null, - "submitter_read_group_id": "D0RH0.2" -} diff --git a/tests/data/seq-exp.bam.metadata.json b/tests/data/seq-exp.bam.metadata.json deleted file mode 100644 index 10ca848..0000000 --- a/tests/data/seq-exp.bam.metadata.json +++ /dev/null @@ -1,73 +0,0 @@ -{ - "type": "sequencing_experiment", - "program_id": "TEST-PRO", - "submitter_sequencing_experiment_id": "TEST_EXP", - "submitter_donor_id": "HCC1143", - "gender": "Female", - "submitter_specimen_id": "HCC1143_BAM_INPUT", - "tumour_normal_designation": "Cell line - derived from normal", - "specimen_tissue_source": "Blood derived", - "submitter_sample_id": "HCC1143_BAM_INPUT", - "sample_type": "DNA", - "submitter_matched_normal_sample_id": null, - "sequencing_center": "EXT", - "platform": "ILLUMINA", - "platform_model": "HiSeq 2000", - "library_strategy": "WGS", - "sequencing_date": "2014-12-12", - "read_group_count": 3, - "read_groups": [ - { - "type": "read_group", - "submitter_read_group_id": "C0HVY.2", - "submitter_sequencing_experiment_id": "TEST_EXP", - "platform_unit": "74_8a", - "is_paired_end": true, - "file_r1": "test_rg_3.bam", - "file_r2": "test_rg_3.bam", - "read_length_r1": 150, - "read_length_r2": 150, - "insert_size": 298, - "sample_barcode": "", - "library_name": "Pond-147580" - }, - { - "type": "read_group", - "submitter_read_group_id": "D0RE2.1", - "submitter_sequencing_experiment_id": "TEST_EXP", - "platform_unit": "74_8b", - "is_paired_end": true, - "file_r1": "test_rg_3.bam", - "file_r2": "test_rg_3.bam", - "read_length_r1": 150, - "read_length_r2": 150, - "insert_size": 298, - "sample_barcode": "", - "library_name": "Pond-147580" - }, - { - "type": "read_group", - "submitter_read_group_id": "D0RH0.2", - "submitter_sequencing_experiment_id": "TEST_EXP", - "platform_unit": "74_8c", - "is_paired_end": true, - "file_r1": "test_rg_3.bam", - "file_r2": "test_rg_3.bam", - "read_length_r1": 150, - "read_length_r2": 150, - "insert_size": 298, - "sample_barcode": "", - "library_name": "Pond-147580" - } - ], - "files": [ - { - "type": "file", - "name": "test_rg_3.bam", - "format": "BAM", - "size": 14911, - "md5sum": "178f97f7b1ca8bfc28fd5586bdd56799", - "path": "test_rg_3.bam" - } - ] -} diff --git a/tests/data/seq-exp.fq.metadata.json b/tests/data/seq-exp.fq.metadata.json deleted file mode 100644 index eb4208d..0000000 --- a/tests/data/seq-exp.fq.metadata.json +++ /dev/null @@ -1,113 +0,0 @@ -{ - "type": "sequencing_experiment", - "program_id": "TEST-PRO", - "submitter_sequencing_experiment_id": "TEST_EXP", - "submitter_donor_id": "HCC1143", - "gender": "Female", - "submitter_specimen_id": "HCC1143_FASTQ_INPUT", - "tumour_normal_designation": "Cell line - derived from tumour", - "specimen_tissue_source": "Blood derived", - "submitter_sample_id": "HCC1143_FASTQ_INPUT", - "sample_type": "DNA", - "submitter_matched_normal_sample_id": "HCC1143_BAM_INPUT", - "sequencing_center": "EXT", - "platform": "ILLUMINA", - "platform_model": "HiSeq 2000", - "library_strategy": "WGS", - "sequencing_date": "2014-12-12", - "read_group_count": 3, - "read_groups": [ - { - "type": "read_group", - "submitter_read_group_id": "C0HVY.2", - "submitter_sequencing_experiment_id": "TEST_EXP", - "platform_unit": "74_8a", - "is_paired_end": true, - "file_r1": "C0HVY.2_r1.fq", - "file_r2": "C0HVY.2_r2.fq", - "read_length_r1": 150, - "read_length_r2": 150, - "insert_size": 298, - "sample_barcode": "", - "library_name": "Pond-147580" - }, - { - "type": "read_group", - "submitter_read_group_id": "D0RE2.1", - "submitter_sequencing_experiment_id": "TEST_EXP", - "platform_unit": "74_8b", - "is_paired_end": true, - "file_r1": 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