diff --git a/fixtures/tests/08944_B.argos.input.json b/fixtures/tests/08944_B.argos.input.json index c64c72527..5ec24b45f 100644 --- a/fixtures/tests/08944_B.argos.input.json +++ b/fixtures/tests/08944_B.argos.input.json @@ -23,6 +23,7 @@ } ], "bam": [], + "zBam": [], "RG_ID": [ "s_C_MP76JR_X001_d_H3MV7BBXY" ], @@ -55,6 +56,7 @@ } ], "bam": [], + "zBam": [], "RG_ID": [ "s_C_MP76JR_N001_d_H3MV7BBXY" ], @@ -392,6 +394,7 @@ } ], "bam": [], + "zBam": [], "RG_ID": [ "s_C_4LM16H_X001_d_H3MV7BBXY" ], diff --git a/fixtures/tests/argos_16342_B_pdx.inputs.json b/fixtures/tests/argos_16342_B_pdx.inputs.json index b9275e4e0..59c99f9a2 100644 --- a/fixtures/tests/argos_16342_B_pdx.inputs.json +++ b/fixtures/tests/argos_16342_B_pdx.inputs.json @@ -1,376 +1,378 @@ -{ - "tumor": { - "ID": "s_C_V5AJEY_P001_d01", - "CN": "MSKCC", - "LB": "16342_B_1", - "PL": "Illumina", - "PU": [ - "HLYCVDSXC", - "HLYCVDSXC" - ], - "R1": [], - "R2": [], - "zR1": [ +[ + { + "tumor": { + "ID": "s_C_V5AJEY_P001_d01", + "CN": "MSKCC", + "LB": "16342_B_1", + "PL": "Illumina", + "PU": [ + "HLYCVDSXC", + "HLYCVDSXC" + ], + "R1": [], + "R2": [], + "zR1": [ + { + "class": "File", + "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R1_001.fastq.gz" + }, + { + "class": "File", + "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz" + } + ], + "zR2": [ + { + "class": "File", + "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz" + }, + { + "class": "File", + "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R2_001.fastq.gz" + } + ], + "bam": [], + "zBam": [], + "RG_ID": [ + "s_C_V5AJEY_P001_d01_HLYCVDSXC", + "s_C_V5AJEY_P001_d01_HLYCVDSXC" + ], + "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", + "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", + "bwa_output": "s_C_V5AJEY_P001_d01.bam", + "request_id": "16342_B", + "specimen_type": "PDX" + }, + "normal": { + "ID": "s_C_V5AJEY_N901_dZ_IM7", + "CN": "MSKCC", + "LB": "C-V5AJEY-N901-dZ-IM7_1", + "PL": "Illumina", + "PU": [ + "DMP_FCID_DMP_BARCODEIDX" + ], + "R1": [], + "R2": [], + "zR1": [], + "zR2": [], + "bam": [], + "zBam": [ + { + "class": "File", + "location": "juno:///juno/dmp/share/irb12_245/J/D/JD536007-N.bam" + } + ], + "RG_ID": [ + "s_C_V5AJEY_N901_dZ_IM7_DMP_FCID_DMP_BARCODEIDX" + ], + "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", + "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", + "bwa_output": "s_C_V5AJEY_N901_dZ_IM7.bam", + "request_id": null, + "specimen_type": "DMP" + }, + "assay": "IMPACT505_BAITS", + "pi": "Adam Schoenfeld", + "pi_email": "", + "patient_id": "C-V5AJEY", + "curated_bams": [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R1_001.fastq.gz" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006708_N001_d.Group9.rg.md.abra.printreads.bam" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz" - } - ], - "zR2": [ + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006709_N001_d.Group11.rg.md.abra.printreads.bam" + }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006710_N001_d.Group5.rg.md.abra.printreads.bam" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R2_001.fastq.gz" - } - ], - "bam": [], - "zBam": [], - "RG_ID": [ - "s_C_V5AJEY_P001_d01_HLYCVDSXC", - "s_C_V5AJEY_P001_d01_HLYCVDSXC" - ], - "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", - "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_V5AJEY_P001_d01.bam", - "request_id": "16342_B", - "specimen_type": "PDX" - }, - "normal": { - "ID": "s_C_V5AJEY_N901_dZ_IM7", - "CN": "MSKCC", - "LB": "C-V5AJEY-N901-dZ-IM7_1", - "PL": "Illumina", - "PU": [ - "DMP_FCID_DMP_BARCODEIDX" - ], - "R1": [], - "R2": [], - "zR1": [], - "zR2": [], - "bam": [], - "zBam": [ + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006711_N001_d.Group7.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006713_N001_d.Group10.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006714_N001_d.Group8.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006715_N001_d.Group6.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006716_N001_d.Group4.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006717_N001_d.Group3.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006718_N001_d.Group1.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_09TAFV_N001_d.Group20.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_1FPU8J_N001_d.Group10.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_29F7HE_N001_d.Group17.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_2J273K_N001_d.Group22.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_32WX55_N001_d.Group17.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_3WFCFP_N001_d.Group24.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_4XFY8V_N001_d.Group2.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_7XDAJW_N001_d.Group15.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_96X4FW_N001_d.Group13.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_A8N9WX_N001_d.Group12.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_CTR0E9_N001_d.Group25.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_DJE4C0_N001_d.Group8.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_FDR1YC_N001_d.Group27.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_FWK8C0_N001_d.Group8.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_HRE3UJ_N001_d.Group9.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_JFM1K9_N001_d.Group3.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_JWYL4J_N001_d.Group19.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_KAT85C_N001_d.Group15.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_LC80PX_N001_d.Group7.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_LNNV52_N001_d.Group26.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_MWF8PH_N001_d.Group6.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_NJHH88_N001_d.Group16.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_NR3W32_N001_d.Group21.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_P10A8A_N001_d.Group29.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_U53DXH_N001_d.Group1.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_U8A7CR_N001_d.Group14.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_VXC8TK_N001_d.Group24.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_W0TXP0_N001_d.Group22.rg.md.abra.printreads.bam" + }, + { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_WWTK32_N001_d.Group18.rg.md.abra.printreads.bam" + }, { "class": "File", - "location": "juno:///juno/dmp/share/irb12_245/J/D/JD536007-N.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_XXC7N6_N001_d.Group12.rg.md.abra.printreads.bam" } ], - "RG_ID": [ - "s_C_V5AJEY_N901_dZ_IM7_DMP_FCID_DMP_BARCODEIDX" - ], - "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", - "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_V5AJEY_N901_dZ_IM7.bam", - "request_id": null, - "specimen_type": "DMP" - }, - "assay": "IMPACT505_BAITS", - "pi": "Adam Schoenfeld", - "pi_email": "", - "patient_id": "C-V5AJEY", - "curated_bams": [ - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006708_N001_d.Group9.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006709_N001_d.Group11.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006710_N001_d.Group5.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006711_N001_d.Group7.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006713_N001_d.Group10.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006714_N001_d.Group8.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006715_N001_d.Group6.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006716_N001_d.Group4.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006717_N001_d.Group3.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006718_N001_d.Group1.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_09TAFV_N001_d.Group20.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_1FPU8J_N001_d.Group10.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_29F7HE_N001_d.Group17.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_2J273K_N001_d.Group22.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_32WX55_N001_d.Group17.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_3WFCFP_N001_d.Group24.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_4XFY8V_N001_d.Group2.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_7XDAJW_N001_d.Group15.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_96X4FW_N001_d.Group13.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_A8N9WX_N001_d.Group12.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_CTR0E9_N001_d.Group25.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_DJE4C0_N001_d.Group8.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_FDR1YC_N001_d.Group27.rg.md.abra.printreads.bam" - }, - { + "hapmap": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_FWK8C0_N001_d.Group8.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/hapmap/hapmap_3.3.b37.vcf" }, - { + "dbsnp": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_HRE3UJ_N001_d.Group9.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/dbsnp/dbsnp_138.b37.excluding_sites_after_129.vcf" }, - { + "indels_1000g": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_JFM1K9_N001_d.Group3.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/indels_1000g/Mills_and_1000G_gold_standard.indels.b37.vcf" }, - { + "snps_1000g": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_JWYL4J_N001_d.Group19.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/snps_1000g/1000G_phase1.snps.high_confidence.b37.vcf" }, - { + "cosmic": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_KAT85C_N001_d.Group15.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/cosmic/CosmicCodingMuts_v67_b37_20131024__NDS.vcf" }, - { + "exac_filter": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_LC80PX_N001_d.Group7.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/vep/cache/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz" }, - { + "ref_fasta": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_LNNV52_N001_d.Group26.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/fasta/b37.fasta" }, - { + "mouse_fasta": { "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_MWF8PH_N001_d.Group6.rg.md.abra.printreads.bam" + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCm38/GRCm38.fasta" }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_NJHH88_N001_d.Group16.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_NR3W32_N001_d.Group21.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_P10A8A_N001_d.Group29.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_U53DXH_N001_d.Group1.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_U8A7CR_N001_d.Group14.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_VXC8TK_N001_d.Group24.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_W0TXP0_N001_d.Group22.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_WWTK32_N001_d.Group18.rg.md.abra.printreads.bam" - }, - { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_XXC7N6_N001_d.Group12.rg.md.abra.printreads.bam" - } - ], - "hapmap": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/hapmap/hapmap_3.3.b37.vcf" - }, - "dbsnp": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/dbsnp/dbsnp_138.b37.excluding_sites_after_129.vcf" - }, - "indels_1000g": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/indels_1000g/Mills_and_1000G_gold_standard.indels.b37.vcf" - }, - "snps_1000g": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/snps_1000g/1000G_phase1.snps.high_confidence.b37.vcf" - }, - "cosmic": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/cosmic/CosmicCodingMuts_v67_b37_20131024__NDS.vcf" - }, - "exac_filter": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/vep/cache/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz" - }, - "ref_fasta": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/fasta/b37.fasta" - }, - "mouse_fasta": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCm38/GRCm38.fasta" - }, - "db_files": { - "refseq": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/refseq/refGene_b37.sorted.txt" - }, - "vep_data": "/var/cache", - "hotspot_list": "/usr/bin/ngs-filters/data/hotspot-list-union-v1-v2.txt", - "hotspot_list_maf": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/qc_resources/hotspot-list-union-v1-v2.maf" - }, - "delly_exclude": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/delly/human.hg19.excl.tsv" - }, - "hotspot_vcf": "/usr/bin/basicfiltering/data/hotspot-list-union-v1-v2.vcf", - "facets_snps": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/facets_snps/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf.gz" - }, - "custom_enst": "/usr/bin/vcf2maf/data/isoform_overrides_at_mskcc", - "vep_path": "/usr/bin/vep", - "conpair_markers": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt", - "conpair_markers_bed": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed", - "bait_intervals": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_b37_baits.ilist" - }, - "target_intervals": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_b37_targets.ilist" - }, - "fp_intervals": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_FP_tiling_intervals.intervals" + "db_files": { + "refseq": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/request_files/refseq/refGene_b37.sorted.txt" + }, + "vep_data": "/var/cache", + "hotspot_list": "/usr/bin/ngs-filters/data/hotspot-list-union-v1-v2.txt", + "hotspot_list_maf": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/qc_resources/hotspot-list-union-v1-v2.maf" + }, + "delly_exclude": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/delly/human.hg19.excl.tsv" + }, + "hotspot_vcf": "/usr/bin/basicfiltering/data/hotspot-list-union-v1-v2.vcf", + "facets_snps": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomes/GRCh37/facets_snps/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf.gz" + }, + "custom_enst": "/usr/bin/vcf2maf/data/isoform_overrides_at_mskcc", + "vep_path": "/usr/bin/vep", + "conpair_markers": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt", + "conpair_markers_bed": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed", + "bait_intervals": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_b37_baits.ilist" + }, + "target_intervals": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_b37_targets.ilist" + }, + "fp_intervals": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_FP_tiling_intervals.intervals" + }, + "fp_genotypes": { + "class": "File", + "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_FP_tiling_genotypes.txt" + } }, - "fp_genotypes": { - "class": "File", - "location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_FP_tiling_genotypes.txt" + "runparams": { + "abra_scratch": "/scratch", + "abra_ram_min": 84000, + "genome": "GRCh37", + "intervals": [ + "1", + "2", + "3", + "4", + "5", + "6", + "7", + "8", + "9", + "10", + "11", + "12", + "13", + "14", + "15", + "16", + "17", + "18", + "19", + "20", + "21", + "22", + "X", + "Y", + "MT" + ], + "mutect_dcov": 50000, + "mutect_rf": [ + "BadCigar" + ], + "num_cpu_threads_per_data_thread": 6, + "covariates": [ + "CycleCovariate", + "ContextCovariate", + "ReadGroupCovariate", + "QualityScoreCovariate" + ], + "emit_original_quals": true, + "num_threads": 10, + "assay": "IMPACT505_BAITS", + "tmp_dir": "/scratch", + "project_prefix": "16342_B", + "opt_dup_pix_dist": "2500", + "delly_type": [ + "DUP", + "DEL", + "INV", + "INS", + "BND" + ], + "facets_cval": 50, + "facets_pcval": 100, + "complex_nn": 0.2, + "complex_tn": 0.5, + "scripts_bin": "/usr/bin", + "gatk_jar_path": "/usr/bin/gatk.jar", + "pi": "Adam Schoenfeld", + "pi_email": "" } - }, - "runparams": { - "abra_scratch": "/scratch", - "abra_ram_min": 84000, - "genome": "GRCh37", - "intervals": [ - "1", - "2", - "3", - "4", - "5", - "6", - "7", - "8", - "9", - "10", - "11", - "12", - "13", - "14", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "X", - "Y", - "MT" - ], - "mutect_dcov": 50000, - "mutect_rf": [ - "BadCigar" - ], - "num_cpu_threads_per_data_thread": 6, - "covariates": [ - "CycleCovariate", - "ContextCovariate", - "ReadGroupCovariate", - "QualityScoreCovariate" - ], - "emit_original_quals": true, - "num_threads": 10, - "assay": "IMPACT505_BAITS", - "tmp_dir": "/scratch", - "project_prefix": "16342_B", - "opt_dup_pix_dist": "2500", - "delly_type": [ - "DUP", - "DEL", - "INV", - "INS", - "BND" - ], - "facets_cval": 50, - "facets_pcval": 100, - "complex_nn": 0.2, - "complex_tn": 0.5, - "scripts_bin": "/usr/bin", - "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "Adam Schoenfeld", - "pi_email": "" } -} \ No newline at end of file +] \ No newline at end of file diff --git a/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py b/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py index 6611ff43c..c030bdbee 100644 --- a/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py +++ b/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py @@ -141,7 +141,7 @@ def test_construct_argos_jobs_bam_pdx(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "argos_16342_B_pdx.inputs.json"))) print("Running test_construct_argos_jobs_pdx") - self.assertTrue(argos_inputs[0] == expected_inputs) + self.assertTrue(argos_inputs == expected_inputs) def test_construct_argos_jobs_bam_non_pdx(self): test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "16342_B.fixtures_non_pdx.json") @@ -181,4 +181,4 @@ def test_construct_argos_jobs_bam_non_pdx(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "argos_16342_B_non_pdx.inputs.json"))) print("Running test_construct_argos_jobs_bam_non_pdx") - self.assertTrue(argos_inputs[0] == expected_inputs) + self.assertTrue(argos_inputs == expected_inputs)