Skip to content

Commit

Permalink
ArgosOperator 2.1.0
Browse files Browse the repository at this point in the history
  • Loading branch information
sivkovic committed Jan 14, 2025
1 parent 2464cfb commit c03f77f
Show file tree
Hide file tree
Showing 13 changed files with 4,264 additions and 7 deletions.
740 changes: 740 additions & 0 deletions fixtures/tests/08944_B.argos.input.json

Large diffs are not rendered by default.

954 changes: 954 additions & 0 deletions fixtures/tests/08944_B.fixtures.json

Large diffs are not rendered by default.

371 changes: 371 additions & 0 deletions fixtures/tests/10075_D_single_TN_pair.argos_1_7_0.input.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,371 @@
[
{
"tumor": {
"ID": "s_C_8VK0V7_R001_d",
"CN": "MSKCC",
"LB": "10075_D_5_1_1_1",
"PL": "Illumina",
"PU": [
"HFTCNBBXY_GTATTGGC-TTGTCGGT"
],
"R1": [
{
"class": "File",
"location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz"
}
],
"R2": [
{
"class": "File",
"location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R2_001.fastq.gz"
}
],
"zR1": [],
"zR2": [],
"bam": [],
"RG_ID": [
"s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"
],
"adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG",
"adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"bwa_output": "s_C_8VK0V7_R001_d.bam",
"request_id": "10075_D",
"specimen_type": "Local Recurrence"
},
"normal": {
"ID": "s_C_8VK0V7_N001_d",
"CN": "MSKCC",
"LB": "10075_D_3",
"PL": "Illumina",
"PU": [
"HCYYWBBXY"
],
"R1": [
{
"class": "File",
"location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R1_001.fastq.gz"
}
],
"R2": [
{
"class": "File",
"location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R2_001.fastq.gz"
}
],
"zR1": [],
"zR2": [],
"bam": [],
"RG_ID": [
"s_C_8VK0V7_N001_d_HCYYWBBXY"
],
"adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG",
"adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"bwa_output": "s_C_8VK0V7_N001_d.bam",
"request_id": "10075_D",
"specimen_type": "Normal"
},
"assay": "IMPACT468_BAITS",
"pi": "John Smith",
"pi_email": "[email protected]",
"patient_id": "C-8VK0V7",
"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"
},
{
"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:///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/IMPACT468/b37/picard_baits.interval_list"
},
"target_intervals": {
"class": "File",
"location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/picard_targets.interval_list"
},
"fp_intervals": {
"class": "File",
"location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/FP_tiling_intervals.list"
},
"fp_genotypes": {
"class": "File",
"location": "juno:///rtsess01/compute/juno/bic/juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/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": "IMPACT468_BAITS",
"tmp_dir": "/scratch",
"project_prefix": "10075_D",
"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": "John Smith",
"pi_email": "[email protected]"
}
}
]
1 change: 1 addition & 0 deletions runner/operator/argos_operator/v2_1_0/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
from .argos_operator import ArgosOperator
Loading

0 comments on commit c03f77f

Please sign in to comment.