From 7f064639fdc67d679e8814d607c53a63d0758bd7 Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Tue, 14 Nov 2023 13:11:07 -0500 Subject: [PATCH 1/4] Add tool level walltime configuration --- runner/models.py | 1 + runner/tasks.py | 2 ++ 2 files changed, 3 insertions(+) diff --git a/runner/models.py b/runner/models.py index 9e2bfee28..ce974ff25 100644 --- a/runner/models.py +++ b/runner/models.py @@ -70,6 +70,7 @@ class Pipeline(BaseModel): operator = models.ForeignKey(Operator, on_delete=models.SET_NULL, null=True, blank=True) default = models.BooleanField(default=False) walltime = models.IntegerField(blank=True, null=True) + tool_walltime = models.IntegerField(blank=True, null=True) memlimit = models.CharField(blank=True, null=True, max_length=20) config = models.CharField(blank=True, null=True, max_length=1000, default=None) diff --git a/runner/tasks.py b/runner/tasks.py index c7db0c78e..400850ea6 100644 --- a/runner/tasks.py +++ b/runner/tasks.py @@ -492,6 +492,8 @@ def submit_job(run_id, output_directory=None, execution_id=None, log_directory=N url = settings.RIDGEBACK_URL + "/v0/jobs/" if run.app.walltime: job["walltime"] = run.app.walltime + if run.app.tool_walltime: + job["tool_walltime"] = run.app.tool_walltime if run.app.memlimit: job["memlimit"] = run.app.memlimit if run.app.output_permission: From 413dbe29353cc2cca57d42dde297cb3b0f41aca0 Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Tue, 14 Nov 2023 13:11:34 -0500 Subject: [PATCH 2/4] Add migration for tool level walltime --- runner/migrations/0058_auto_20231114_1310.py | 28 ++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 runner/migrations/0058_auto_20231114_1310.py diff --git a/runner/migrations/0058_auto_20231114_1310.py b/runner/migrations/0058_auto_20231114_1310.py new file mode 100644 index 000000000..214564743 --- /dev/null +++ b/runner/migrations/0058_auto_20231114_1310.py @@ -0,0 +1,28 @@ +# Generated by Django 2.2.28 on 2023-11-14 18:10 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('runner', '0057_auto_20230424_0743'), + ] + + operations = [ + migrations.AddField( + model_name='pipeline', + name='tool_walltime', + field=models.IntegerField(blank=True, null=True), + ), + migrations.AlterField( + model_name='run', + name='restart_attempts', + field=models.IntegerField(default=0), + ), + migrations.AlterField( + model_name='run', + name='resume_attempts', + field=models.IntegerField(default=3), + ), + ] From f6ec3ee86cfc7950550359358f563f1b8185976d Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Tue, 14 Nov 2023 13:12:45 -0500 Subject: [PATCH 3/4] Added black formatting --- input1.json | 377 +++++++++++++++++++ runner/migrations/0058_auto_20231114_1310.py | 14 +- 2 files changed, 384 insertions(+), 7 deletions(-) create mode 100644 input1.json diff --git a/input1.json b/input1.json new file mode 100644 index 000000000..433677274 --- /dev/null +++ b/input1.json @@ -0,0 +1,377 @@ +{ + "pair": [ + { + "CN": "MSKCC", + "ID": "s_EP300_KO_2_14122B", + "LB": "14122_B_1_1_1_1", + "PL": "Illumina", + "PU": [ + "HJFW7DMXY", + "HH7FKDSX5" + ], + "R1": [ + { + "path": "/juno/archive/msk/cmo/FASTQ/DIANA_0580_BHJFW7DMXY/Project_14122_B/Sample_EP300_KO_2_IGO_14122_B_1/EP300_KO_2_IGO_14122_B_1_S18_L001_R1_001.fastq.gz", + "class": "File" + }, + { + "path": "/juno/archive/msk/cmo/FASTQ/DIANA_0578_BHH7FKDSX5/Project_14122_B/Sample_EP300_KO_2_IGO_14122_B_1/EP300_KO_2_IGO_14122_B_1_S74_L002_R1_001.fastq.gz", + "class": "File" + } + ], + "R2": [ + { + "path": "/juno/archive/msk/cmo/FASTQ/DIANA_0580_BHJFW7DMXY/Project_14122_B/Sample_EP300_KO_2_IGO_14122_B_1/EP300_KO_2_IGO_14122_B_1_S18_L001_R2_001.fastq.gz", + "class": "File" + }, + { + "path": "/juno/archive/msk/cmo/FASTQ/DIANA_0578_BHH7FKDSX5/Project_14122_B/Sample_EP300_KO_2_IGO_14122_B_1/EP300_KO_2_IGO_14122_B_1_S74_L002_R2_001.fastq.gz", + "class": "File" + } + ], + "bam": [], + "zR1": [], + "zR2": [], + "RG_ID": [ + "s_EP300_KO_2_14122B_HJFW7DMXY", + "s_EP300_KO_2_14122B_HH7FKDSX5" + ], + "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", + "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", + "bwa_output": "s_EP300_KO_2_14122B.bam", + "request_id": "14122_B", + "specimen_type": "CellLine" + }, + { + "CN": "MSKCC", + "ID": "FROZENPOOLEDNORMAL_IMPACT505_V2", + "LB": "FROZENPOOLEDNORMAL_IMPACT505_V2_1", + "PL": "Illumina", + "PU": [ + "PN_FCID_FROZENPOOLEDNORMAL_IGO_IMPACT505_CTGATTGA_S158_L002__001" + ], + "R1": [ + { + "path": "/juno/archive/msk/cmo/ci/resources/PooledNormals/IMPACT505/FROZEN/Sample_FROZENPOOLEDNORMAL_IMPACT505_V2/FROZENPOOLEDNORMAL_IGO_IMPACT505_CTGATTGA_S158_L002_R1_001.fastq.gz", + "class": "File" + } + ], + "R2": [ + { + "path": "/juno/archive/msk/cmo/ci/resources/PooledNormals/IMPACT505/FROZEN/Sample_FROZENPOOLEDNORMAL_IMPACT505_V2/FROZENPOOLEDNORMAL_IGO_IMPACT505_CTGATTGA_S158_L002_R2_001.fastq.gz", + "class": "File" + } + ], + "bam": [], + "zR1": [], + "zR2": [], + "RG_ID": [ + "FROZENPOOLEDNORMAL_IMPACT505_V2_PN_FCID_FROZENPOOLEDNORMAL_IGO_IMPACT505_CTGATTGA_S158_L002__001" + ], + "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", + "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", + "bwa_output": "FROZENPOOLEDNORMAL_IMPACT505_V2.bam", + "request_id": "FROZENPOOLEDNORMAL_IMPACT505_V2", + "specimen_type": "Pooled Normal" + } + ], + "dbsnp": { + "path": "/juno/work/ci/resources/request_files/dbsnp/dbsnp_138.b37.excluding_sites_after_129.vcf", + "class": "File" + }, + "cosmic": { + "path": "/juno/work/ci/resources/request_files/cosmic/CosmicCodingMuts_v67_b37_20131024__NDS.vcf", + "class": "File" + }, + "hapmap": { + "path": "/juno/work/ci/resources/request_files/hapmap/hapmap_3.3.b37.vcf", + "class": "File" + }, + "db_files": { + "refseq": { + "path": "/juno/work/ci/resources/request_files/refseq/refGene_b37.sorted.txt", + "class": "File" + }, + "vep_data": "/var/cache", + "vep_path": "/usr/bin/vep", + "custom_enst": "/usr/bin/vcf2maf/data/isoform_overrides_at_mskcc", + "facets_snps": { + "path": "/juno/work/ci/resources/genomes/GRCh37/facets_snps/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf.gz", + "class": "File" + }, + "hotspot_vcf": "/usr/bin/basicfiltering/data/hotspot-list-union-v1-v2.vcf", + "fp_genotypes": { + "path": "/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_FP_tiling_genotypes.txt", + "class": "File" + }, + "fp_intervals": { + "path": "/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_FP_tiling_intervals.intervals", + "class": "File" + }, + "hotspot_list": "/usr/bin/ngs-filters/data/hotspot-list-union-v1-v2.txt", + "delly_exclude": { + "path": "/juno/work/ci/resources/genomes/GRCh37/delly/human.hg19.excl.tsv", + "class": "File" + }, + "bait_intervals": { + "path": "/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_b37_baits.ilist", + "class": "File" + }, + "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", + "hotspot_list_maf": { + "path": "/juno/work/ci/resources/qc_resources/hotspot-list-union-v1-v2.maf", + "class": "File" + }, + "target_intervals": { + "path": "/juno/work/ci/resources/genomic_resources/targets/IMPACT505/b37/IMPACT505_b37_targets.ilist", + "class": "File" + }, + "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" + }, + "ref_fasta": { + "path": "/juno/work/ci/resources/genomes/GRCh37/fasta/b37.fasta", + "class": "File" + }, + "runparams": { + "pi": "David Solit", + "assay": "IMPACT505_BAITS", + "genome": "GRCh37", + "tmp_dir": "/scratch", + "pi_email": "solitd@mskcc.org", + "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_rf": [ + "BadCigar" + ], + "complex_nn": 0.2, + "complex_tn": 0.5, + "covariates": [ + "CycleCovariate", + "ContextCovariate", + "ReadGroupCovariate", + "QualityScoreCovariate" + ], + "delly_type": [ + "DUP", + "DEL", + "INV", + "INS", + "BND" + ], + "facets_cval": 50, + "mutect_dcov": 50000, + "num_threads": 10, + "scripts_bin": "/usr/bin", + "abra_ram_min": 84000, + "abra_scratch": "/scratch", + "facets_pcval": 100, + "gatk_jar_path": "/usr/bin/gatk.jar", + "project_prefix": "14122_B", + "opt_dup_pix_dist": "2500", + "emit_original_quals": true, + "num_cpu_threads_per_data_thread": 6 + }, + "snps_1000g": { + "path": "/juno/work/ci/resources/request_files/snps_1000g/1000G_phase1.snps.high_confidence.b37.vcf", + "class": "File" + }, + "exac_filter": { + "path": "/juno/work/ci/resources/vep/cache/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz", + "class": "File" + }, + "mouse_fasta": { + "path": "/juno/work/ci/resources/genomes/GRCm38/GRCm38.fasta", + "class": "File" + }, + "curated_bams": [ + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006708_N001_d.Group9.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006709_N001_d.Group11.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006710_N001_d.Group5.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006711_N001_d.Group7.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006713_N001_d.Group10.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006714_N001_d.Group8.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006715_N001_d.Group6.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006716_N001_d.Group4.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006717_N001_d.Group3.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_006718_N001_d.Group1.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_09TAFV_N001_d.Group20.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_1FPU8J_N001_d.Group10.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": 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"/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_P10A8A_N001_d.Group29.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_U53DXH_N001_d.Group1.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_U8A7CR_N001_d.Group14.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_VXC8TK_N001_d.Group24.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_W0TXP0_N001_d.Group22.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_WWTK32_N001_d.Group18.rg.md.abra.printreads.bam", + "class": "File" + }, + { + "path": "/juno/work/ci/resources/curated_bams/IMPACT468_b37/s_C_XXC7N6_N001_d.Group12.rg.md.abra.printreads.bam", + "class": "File" + } + ], + "indels_1000g": { + "path": "/juno/work/ci/resources/request_files/indels_1000g/Mills_and_1000G_gold_standard.indels.b37.vcf", + "class": "File" + } +} \ No newline at end of file diff --git a/runner/migrations/0058_auto_20231114_1310.py b/runner/migrations/0058_auto_20231114_1310.py index 214564743..6dccc8365 100644 --- a/runner/migrations/0058_auto_20231114_1310.py +++ b/runner/migrations/0058_auto_20231114_1310.py @@ -6,23 +6,23 @@ class Migration(migrations.Migration): dependencies = [ - ('runner', '0057_auto_20230424_0743'), + ("runner", "0057_auto_20230424_0743"), ] operations = [ migrations.AddField( - model_name='pipeline', - name='tool_walltime', + model_name="pipeline", + name="tool_walltime", field=models.IntegerField(blank=True, null=True), ), migrations.AlterField( - model_name='run', - name='restart_attempts', + model_name="run", + name="restart_attempts", field=models.IntegerField(default=0), ), migrations.AlterField( - model_name='run', - name='resume_attempts', + model_name="run", + name="resume_attempts", field=models.IntegerField(default=3), ), ] From 061c806b1a2c6ef24d434f763c79d073fd8b8203 Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Tue, 14 Nov 2023 13:49:52 -0500 Subject: [PATCH 4/4] Some cleanup --- input1.json | 377 ---------------------------------------------------- 1 file changed, 377 deletions(-) delete mode 100644 input1.json diff --git a/input1.json b/input1.json deleted file mode 100644 index 433677274..000000000 --- a/input1.json +++ /dev/null @@ -1,377 +0,0 @@ -{ - "pair": [ - { - "CN": "MSKCC", - "ID": "s_EP300_KO_2_14122B", - "LB": "14122_B_1_1_1_1", - "PL": "Illumina", - "PU": [ - "HJFW7DMXY", - "HH7FKDSX5" - ], - "R1": [ - { - "path": "/juno/archive/msk/cmo/FASTQ/DIANA_0580_BHJFW7DMXY/Project_14122_B/Sample_EP300_KO_2_IGO_14122_B_1/EP300_KO_2_IGO_14122_B_1_S18_L001_R1_001.fastq.gz", - "class": "File" - }, - { - "path": 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