diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json index 596f1fc..92146c1 100644 --- a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json +++ b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json @@ -10,8 +10,8 @@ [] ], "config__algorithm__align_split_size": [ - "False", - "False" + null, + null ], "config__algorithm__aligner": [ "bwa", @@ -33,8 +33,8 @@ null ], "config__algorithm__effects": [ - "False", - "False" + "snpeff", + "snpeff" ], "config__algorithm__ensemble": [ null, @@ -49,8 +49,8 @@ "True" ], "config__algorithm__min_allele_fraction": [ - 10, - 10 + 10.0, + 10.0 ], "config__algorithm__nomap_split_size": [ 250, @@ -87,12 +87,8 @@ "True" ], "config__algorithm__tools_off": [ - [ - "gemini" - ], - [ - "gemini" - ] + [], + [] ], "config__algorithm__tools_on": [ [ @@ -348,6 +344,28 @@ ] } ], + "genome_resources__variation__gnomad_exome": [ + { + "class": "File", + "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz", + "secondaryFiles": [ + { + "class": "File", + "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi" + } + ] + }, + { + "class": "File", + "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz", + "secondaryFiles": [ + { + "class": "File", + "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi" + } + ] + } + ], "genome_resources__variation__lcr": [ null, null @@ -550,14 +568,14 @@ "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz" } ], - "reference__twobit": [ + "reference__versions": [ { "class": "File", - "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/ucsc/hg19.2bit" + "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/versions.csv" }, { "class": "File", - "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/ucsc/hg19.2bit" + "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/versions.csv" } ], "resources": [ diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl index 05ee299..69c805f 100644 --- a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl +++ b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl @@ -5,9 +5,8 @@ inputs: - id: config__algorithm__align_split_size type: items: - - string - 'null' - - boolean + - string type: array - id: files type: @@ -74,12 +73,6 @@ inputs: type: items: File type: array -- id: genome_resources__variation__train_hapmap - secondaryFiles: - - .tbi - type: - items: File - type: array - id: rgnames__lb type: items: @@ -118,12 +111,16 @@ inputs: type: array - id: config__algorithm__min_allele_fraction type: - items: long + items: double type: array - id: config__algorithm__nomap_split_targets type: items: long type: array +- id: reference__versions + type: + items: File + type: array - id: reference__bwa__indexes secondaryFiles: - ^.ann @@ -139,7 +136,9 @@ inputs: - 'null' - string type: array -- id: reference__twobit +- id: genome_resources__variation__train_hapmap + secondaryFiles: + - .tbi type: items: File type: array @@ -204,6 +203,12 @@ inputs: type: items: File type: array +- id: genome_resources__variation__gnomad_exome + secondaryFiles: + - .tbi + type: + items: File + type: array - id: config__algorithm__recalibrate type: items: @@ -227,7 +232,8 @@ inputs: - id: config__algorithm__tools_off type: items: - items: string + - 'null' + - items: 'null' type: array type: array - id: genome_resources__variation__dbsnp @@ -289,10 +295,7 @@ inputs: type: array - id: config__algorithm__effects type: - items: - - string - - 'null' - - boolean + items: string type: array - id: config__algorithm__variant_regions type: @@ -376,6 +379,20 @@ outputs: - File - 'null' type: array +- id: versions__tools + outputSource: multiqc_summary/versions__tools + type: + items: + - File + - 'null' + type: array +- id: versions__data + outputSource: multiqc_summary/versions__data + type: + items: + - File + - 'null' + type: array requirements: - class: EnvVarRequirement envDef: @@ -416,6 +433,8 @@ steps: source: config__algorithm__adapters - id: config__algorithm__bam_clean source: config__algorithm__bam_clean + - id: config__algorithm__variant_regions + source: config__algorithm__variant_regions - id: config__algorithm__mark_duplicates source: config__algorithm__mark_duplicates - id: resources @@ -431,9 +450,9 @@ steps: source: alignment_to_rec/alignment_rec out: - id: align_bam - - id: hla__fastq - id: work_bam_plus__disc - id: work_bam_plus__sr + - id: hla__fastq run: wf-alignment.cwl scatter: - alignment_rec @@ -508,8 +527,6 @@ steps: source: genome_resources__variation__polyx - id: genome_resources__variation__encode_blacklist source: genome_resources__variation__encode_blacklist - - id: reference__twobit - source: reference__twobit - id: reference__fasta__base source: reference__fasta__base - id: resources @@ -618,8 +635,6 @@ steps: source: config__algorithm__tools_off - id: reference__fasta__base source: reference__fasta__base - - id: reference__twobit - source: reference__twobit - id: reference__rtg source: reference__rtg - id: reference__genome_context @@ -634,6 +649,8 @@ steps: source: genome_resources__variation__esp - id: genome_resources__variation__exac source: genome_resources__variation__exac + - id: genome_resources__variation__gnomad_exome + source: genome_resources__variation__gnomad_exome - id: genome_resources__variation__1000g source: genome_resources__variation__1000g - id: genome_resources__variation__lcr @@ -708,6 +725,8 @@ steps: source: analysis - id: reference__fasta__base source: reference__fasta__base + - id: reference__versions + source: reference__versions - id: config__algorithm__tools_on source: config__algorithm__tools_on - id: config__algorithm__tools_off @@ -718,6 +737,8 @@ steps: source: config__algorithm__qc - id: metadata__batch source: metadata__batch + - id: metadata__phenotype + source: metadata__phenotype - id: config__algorithm__coverage_interval source: postprocess_alignment/config__algorithm__coverage_interval - id: depth__variant_regions__regions @@ -771,4 +792,6 @@ steps: source: pipeline_summary/qcout_rec out: - id: summary__multiqc + - id: versions__tools + - id: versions__data run: steps/multiqc_summary.cwl diff --git a/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl index 1bef8f3..aee319f 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl @@ -4,8 +4,8 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-combined -- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample -- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__mark_duplicates:var,resources:var,description:var +- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions +- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var - run_number=0 baseCommand: - bcbio_nextgen.py @@ -39,9 +39,8 @@ inputs: - id: config__algorithm__align_split_size type: items: - - string - 'null' - - boolean + - string type: array - id: reference__fasta__base secondaryFiles: @@ -112,6 +111,10 @@ inputs: - 'null' - boolean type: array +- id: config__algorithm__variant_regions + type: + items: File + type: array - id: config__algorithm__mark_duplicates type: items: @@ -138,9 +141,8 @@ outputs: type: string - name: config__algorithm__align_split_size type: - - string - 'null' - - boolean + - string - name: files type: items: File @@ -189,6 +191,8 @@ outputs: type: string - name: rgnames__sample type: string + - name: config__algorithm__variant_regions + type: File name: alignment_rec type: record type: array diff --git a/gvcf_joint/gvcf-joint-workflow/steps/batch_for_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/batch_for_jointvc.cwl index bbf8256..581e796 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/batch_for_jointvc.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/batch_for_jointvc.cwl @@ -4,7 +4,7 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-batch -- sentinel_outputs=jointvc_batch_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__train_hapmap;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions +- sentinel_outputs=jointvc_batch_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions - sentinel_inputs=vc_rec:record - run_number=0 baseCommand: @@ -74,8 +74,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -87,7 +85,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -106,6 +106,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -113,7 +115,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -138,10 +141,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File @@ -222,8 +222,6 @@ outputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -235,7 +233,9 @@ outputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -254,6 +254,8 @@ outputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -261,7 +263,8 @@ outputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -286,10 +289,7 @@ outputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/batch_for_variantcall.cwl b/gvcf_joint/gvcf-joint-workflow/steps/batch_for_variantcall.cwl index 077c8d4..886372c 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/batch_for_variantcall.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/batch_for_variantcall.cwl @@ -4,8 +4,8 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-batch -- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__train_hapmap;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;reference__twobit;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions -- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__twobit:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var +- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions +- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var - run_number=0 baseCommand: - bcbio_nextgen.py @@ -92,14 +92,11 @@ inputs: type: array - id: config__algorithm__effects type: - items: - - string - - 'null' - - boolean + items: string type: array - id: config__algorithm__min_allele_fraction type: - items: long + items: double type: array - id: config__algorithm__exclude_regions type: @@ -141,7 +138,8 @@ inputs: - id: config__algorithm__tools_off type: items: - items: string + - 'null' + - items: 'null' type: array type: array - id: reference__fasta__base @@ -151,10 +149,6 @@ inputs: type: items: File type: array -- id: reference__twobit - type: - items: File - type: array - id: reference__rtg type: items: File @@ -197,6 +191,12 @@ inputs: type: items: File type: array +- id: genome_resources__variation__gnomad_exome + secondaryFiles: + - .tbi + type: + items: File + type: array - id: genome_resources__variation__1000g secondaryFiles: - .tbi @@ -286,8 +286,6 @@ outputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -299,12 +297,12 @@ outputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double - name: vrn_file type: - 'null' - string - - name: reference__twobit + - name: genome_resources__variation__train_hapmap type: File - name: reference__genome_context type: @@ -324,6 +322,8 @@ outputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -331,7 +331,8 @@ outputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -356,10 +357,7 @@ outputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/compare_to_rm.cwl b/gvcf_joint/gvcf-joint-workflow/steps/compare_to_rm.cwl index 4430866..64cd4a6 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/compare_to_rm.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/compare_to_rm.cwl @@ -4,7 +4,7 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=batch-single -- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__train_hapmap;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions +- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions - sentinel_inputs=batch_rec:record,vrn_file:var - run_number=0 baseCommand: @@ -73,8 +73,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -86,12 +84,12 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double - name: vrn_file type: - 'null' - string - - name: reference__twobit + - name: genome_resources__variation__train_hapmap type: File - name: reference__genome_context type: @@ -111,6 +109,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -118,7 +118,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -143,10 +144,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File @@ -233,8 +231,6 @@ outputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -246,7 +242,9 @@ outputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -265,6 +263,8 @@ outputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -272,7 +272,8 @@ outputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -297,10 +298,7 @@ outputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl b/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl index 87b8299..5074614 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl @@ -63,8 +63,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -76,12 +74,12 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double - name: vrn_file type: - 'null' - string - - name: reference__twobit + - name: genome_resources__variation__train_hapmap type: File - name: reference__genome_context type: @@ -101,6 +99,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -108,7 +108,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -133,10 +134,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl index 0672f46..b95a4a3 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl @@ -86,8 +86,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -99,7 +97,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -118,6 +118,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -125,7 +127,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -150,10 +153,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/finalize_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/finalize_jointvc.cwl index b53c61e..b9059d7 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/finalize_jointvc.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/finalize_jointvc.cwl @@ -4,7 +4,7 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=batch-single -- sentinel_outputs=jointvc_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__train_hapmap;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions;vrn_file_joint +- sentinel_outputs=jointvc_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions;vrn_file_joint - sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var - run_number=0 baseCommand: @@ -73,8 +73,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -86,7 +84,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -105,6 +105,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -112,7 +114,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -137,10 +140,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File @@ -223,8 +223,6 @@ outputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -236,7 +234,9 @@ outputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -255,6 +255,8 @@ outputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -262,7 +264,8 @@ outputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -287,10 +290,7 @@ outputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions.cwl b/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions.cwl index 336aa4a..32b5599 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions.cwl @@ -50,8 +50,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -63,12 +61,12 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double - name: vrn_file type: - 'null' - string - - name: reference__twobit + - name: genome_resources__variation__train_hapmap type: File - name: reference__genome_context type: @@ -88,6 +86,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -95,7 +95,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -120,10 +121,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl index 748414e..c07b0ab 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl @@ -73,8 +73,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -86,7 +84,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -105,6 +105,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -112,7 +114,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -137,10 +140,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl b/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl new file mode 100644 index 0000000..6680b2c --- /dev/null +++ b/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl @@ -0,0 +1,171 @@ +$namespaces: + dx: https://www.dnanexus.com/cwl# +arguments: +- position: 0 + valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) +- sentinel_parallel=single-merge +- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq +- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var +- run_number=0 +baseCommand: +- bcbio_nextgen.py +- runfn +- merge_split_alignments +- cwl +class: CommandLineTool +cwlVersion: v1.0 +hints: +- class: DockerRequirement + dockerImageId: quay.io/bcbio/bcbio-vc + dockerPull: quay.io/bcbio/bcbio-vc +- class: ResourceRequirement + coresMin: 2 + outdirMin: 1035 + ramMin: 4096 + tmpdirMin: 6 +- class: dx:InputResourceRequirement + indirMin: 4 +- class: SoftwareRequirement + packages: + - package: biobambam + specs: + - https://anaconda.org/bioconda/biobambam + - package: samtools + specs: + - https://anaconda.org/bioconda/samtools + - package: variantbam + specs: + - https://anaconda.org/bioconda/variantbam +inputs: +- id: alignment_rec + type: + fields: + - name: resources + type: string + - name: description + type: string + - name: config__algorithm__align_split_size + type: + - 'null' + - string + - name: files + type: + items: File + type: array + - name: config__algorithm__trim_reads + type: + - string + - 'null' + - boolean + - name: reference__fasta__base + type: File + - name: config__algorithm__adapters + type: + - 'null' + - items: + - 'null' + - string + type: array + - name: rgnames__lb + type: + - 'null' + - string + - name: rgnames__rg + type: string + - name: rgnames__lane + type: string + - name: reference__bwa__indexes + type: File + - name: config__algorithm__bam_clean + type: + - string + - 'null' + - boolean + - name: config__algorithm__aligner + type: string + - name: rgnames__pl + type: string + - name: rgnames__pu + type: string + - name: config__algorithm__mark_duplicates + type: + - string + - 'null' + - boolean + - name: analysis + type: string + - name: rgnames__sample + type: string + - name: config__algorithm__variant_regions + type: File + name: alignment_rec + type: record +- id: work_bam + secondaryFiles: + - .bai + type: + items: + - File + - 'null' + type: array +- id: align_bam_toolinput + secondaryFiles: + - .bai + type: + items: + - File + - 'null' + type: array +- id: work_bam_plus__disc_toolinput + secondaryFiles: + - .bai + type: + items: + - File + - 'null' + type: array +- id: work_bam_plus__sr_toolinput + secondaryFiles: + - .bai + type: + items: + - File + - 'null' + type: array +- id: hla__fastq_toolinput + type: + items: + - 'null' + - items: File + type: array + type: array +outputs: +- id: align_bam + secondaryFiles: + - .bai + type: + - File + - 'null' +- id: work_bam_plus__disc + secondaryFiles: + - .bai + type: + - File + - 'null' +- id: work_bam_plus__sr + secondaryFiles: + - .bai + type: + - File + - 'null' +- id: hla__fastq + type: + - 'null' + - items: File + type: array +requirements: +- class: InlineJavascriptRequirement +- class: InitialWorkDirRequirement + listing: + - entry: $(JSON.stringify(inputs)) + entryname: cwl.inputs.json diff --git a/gvcf_joint/gvcf-joint-workflow/steps/multiqc_summary.cwl b/gvcf_joint/gvcf-joint-workflow/steps/multiqc_summary.cwl index 918ab5d..ad7850d 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/multiqc_summary.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/multiqc_summary.cwl @@ -4,7 +4,7 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-combined -- sentinel_outputs=summary__multiqc +- sentinel_outputs=summary__multiqc,versions__tools,versions__data - sentinel_inputs=qcout_rec:record - run_number=0 baseCommand: @@ -48,11 +48,14 @@ inputs: - 'null' - name: description type: string + - name: reference__versions + type: File - name: genome_build type: string - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: config__algorithm__qc type: @@ -72,6 +75,18 @@ outputs: - File - 'null' type: array +- id: versions__tools + type: + items: + - File + - 'null' + type: array +- id: versions__data + type: + items: + - File + - 'null' + type: array requirements: - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement diff --git a/gvcf_joint/gvcf-joint-workflow/steps/pipeline_summary.cwl b/gvcf_joint/gvcf-joint-workflow/steps/pipeline_summary.cwl index 1e7de68..5fbf2e9 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/pipeline_summary.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/pipeline_summary.cwl @@ -5,7 +5,7 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-parallel -- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on +- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on - sentinel_inputs=qc_rec:record - run_number=0 baseCommand: @@ -34,9 +34,9 @@ hints: - package: bedtools specs: - https://anaconda.org/bioconda/bedtools - - package: fastqc=0.11.7=4 + - package: fastqc=0.11.7=5 specs: - - https://anaconda.org/bioconda/fastqc=0.11.7=4 + - https://anaconda.org/bioconda/fastqc=0.11.7=5 - package: goleft specs: - https://anaconda.org/bioconda/goleft @@ -85,12 +85,16 @@ inputs: type: string - name: reference__fasta__base type: File + - name: metadata__phenotype + type: string - name: config__algorithm__coverage_interval type: - string - 'null' - name: metadata__batch type: string + - name: reference__versions + type: File - name: genome_build type: string - name: config__algorithm__coverage @@ -99,7 +103,8 @@ inputs: - 'null' - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: config__algorithm__qc type: @@ -187,11 +192,14 @@ outputs: - 'null' - name: description type: string + - name: reference__versions + type: File - name: genome_build type: string - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: config__algorithm__qc type: diff --git a/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment.cwl b/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment.cwl index 40f6a3e..77144c5 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment.cwl @@ -70,8 +70,6 @@ inputs: type: - 'null' - string - - name: reference__twobit - type: File - name: config__algorithm__recalibrate type: - string diff --git a/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl b/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl index 69cded1..e10a965 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl @@ -4,8 +4,8 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-combined -- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;reference__twobit;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready -- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__twobit:var,reference__fasta__base:var,resources:var,description:var +- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready +- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var - run_number=0 baseCommand: - bcbio_nextgen.py @@ -130,10 +130,6 @@ inputs: - 'null' - string type: array -- id: reference__twobit - type: - items: File - type: array - id: reference__fasta__base secondaryFiles: - .fai @@ -170,8 +166,6 @@ outputs: type: - 'null' - string - - name: reference__twobit - type: File - name: config__algorithm__recalibrate type: - string diff --git a/gvcf_joint/gvcf-joint-workflow/steps/postprocess_variants.cwl b/gvcf_joint/gvcf-joint-workflow/steps/postprocess_variants.cwl index f62cbac..cc228f5 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/postprocess_variants.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/postprocess_variants.cwl @@ -80,8 +80,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -93,7 +91,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -112,6 +112,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -119,7 +121,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -144,10 +147,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl b/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl index c785b95..00f3447 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl @@ -3,7 +3,7 @@ $namespaces: arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) -- sentinel_parallel=single-single +- sentinel_parallel=single-split - sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split - sentinel_inputs=alignment_rec:record - run_number=0 @@ -62,9 +62,8 @@ inputs: type: string - name: config__algorithm__align_split_size type: - - string - 'null' - - boolean + - string - name: files type: items: File @@ -113,27 +112,31 @@ inputs: type: string - name: rgnames__sample type: string + - name: config__algorithm__variant_regions + type: File name: alignment_rec type: record outputs: - id: process_alignment_rec type: - fields: - - name: files - type: - - 'null' - - items: File - type: array - - name: config__algorithm__quality_format - type: - - string - - 'null' - - name: align_split - type: - - string - - 'null' - name: process_alignment_rec - type: record + items: + fields: + - name: files + type: + - 'null' + - items: File + type: array + - name: config__algorithm__quality_format + type: + - string + - 'null' + - name: align_split + type: + - string + - 'null' + name: process_alignment_rec + type: record + type: array requirements: - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement diff --git a/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl b/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl index 2245b63..c846a48 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl @@ -4,7 +4,7 @@ $namespaces: arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) -- sentinel_parallel=single-single +- sentinel_parallel=single-parallel - sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr - sentinel_inputs=alignment_rec:record,process_alignment_rec:record - run_number=0 @@ -91,9 +91,8 @@ inputs: type: string - name: config__algorithm__align_split_size type: - - string - 'null' - - boolean + - string - name: files type: items: File @@ -142,6 +141,8 @@ inputs: type: string - name: rgnames__sample type: string + - name: config__algorithm__variant_regions + type: File name: alignment_rec type: record - id: process_alignment_rec diff --git a/gvcf_joint/gvcf-joint-workflow/steps/qc_to_rec.cwl b/gvcf_joint/gvcf-joint-workflow/steps/qc_to_rec.cwl index b999e2d..0751be7 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/qc_to_rec.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/qc_to_rec.cwl @@ -4,8 +4,8 @@ arguments: - position: 0 valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram']) - sentinel_parallel=multi-combined -- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples -- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var +- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples +- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var - run_number=0 baseCommand: - bcbio_nextgen.py @@ -45,6 +45,10 @@ inputs: type: items: File type: array +- id: reference__versions + type: + items: File + type: array - id: config__algorithm__tools_on type: items: @@ -54,7 +58,8 @@ inputs: - id: config__algorithm__tools_off type: items: - items: string + - 'null' + - items: 'null' type: array type: array - id: genome_build @@ -71,6 +76,10 @@ inputs: type: items: string type: array +- id: metadata__phenotype + type: + items: string + type: array - id: config__algorithm__coverage_interval type: items: @@ -184,12 +193,16 @@ outputs: type: string - name: reference__fasta__base type: File + - name: metadata__phenotype + type: string - name: config__algorithm__coverage_interval type: - string - 'null' - name: metadata__batch type: string + - name: reference__versions + type: File - name: genome_build type: string - name: config__algorithm__coverage @@ -198,7 +211,8 @@ outputs: - 'null' - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: config__algorithm__qc type: diff --git a/gvcf_joint/gvcf-joint-workflow/steps/run_jointvc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/run_jointvc.cwl index 329d0ed..dfbb027 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/run_jointvc.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/run_jointvc.cwl @@ -31,9 +31,9 @@ hints: - package: gatk4 specs: - https://anaconda.org/bioconda/gatk4 - - package: gvcftools + - package: gvcfgenotyper specs: - - https://anaconda.org/bioconda/gvcftools + - https://anaconda.org/bioconda/gvcfgenotyper - package: sentieon specs: - https://anaconda.org/bioconda/sentieon @@ -86,8 +86,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -99,7 +97,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -118,6 +118,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -125,7 +127,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -150,10 +153,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/summarize_vc.cwl b/gvcf_joint/gvcf-joint-workflow/steps/summarize_vc.cwl index b95e9ea..48b35d5 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/summarize_vc.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/summarize_vc.cwl @@ -74,8 +74,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -87,7 +85,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -106,6 +106,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -113,7 +115,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -138,10 +141,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/steps/variantcall_batch_region.cwl b/gvcf_joint/gvcf-joint-workflow/steps/variantcall_batch_region.cwl index e22fb28..72fa1d6 100644 --- a/gvcf_joint/gvcf-joint-workflow/steps/variantcall_batch_region.cwl +++ b/gvcf_joint/gvcf-joint-workflow/steps/variantcall_batch_region.cwl @@ -86,6 +86,9 @@ hints: - package: varscan specs: - https://anaconda.org/bioconda/varscan + - package: moreutils + specs: + - https://anaconda.org/bioconda/moreutils - package: vcfanno specs: - https://anaconda.org/bioconda/vcfanno @@ -100,6 +103,9 @@ hints: - https://anaconda.org/bioconda/r version: - 3.4.1 + - package: r-base=3.4.1=h4fe35fd_8 + specs: + - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8 - package: perl specs: - https://anaconda.org/bioconda/perl @@ -131,8 +137,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -144,12 +148,12 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double - name: vrn_file type: - 'null' - string - - name: reference__twobit + - name: genome_resources__variation__train_hapmap type: File - name: reference__genome_context type: @@ -169,6 +173,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -176,7 +182,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -201,10 +208,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl b/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl index 02719d5..1cb0144 100644 --- a/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl +++ b/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl @@ -11,9 +11,8 @@ inputs: type: string - name: config__algorithm__align_split_size type: - - string - 'null' - - boolean + - string - name: files type: items: File @@ -62,36 +61,38 @@ inputs: type: string - name: rgnames__sample type: string + - name: config__algorithm__variant_regions + type: File name: alignment_rec type: record outputs: - id: align_bam - outputSource: process_alignment/align_bam + outputSource: merge_split_alignments/align_bam secondaryFiles: - .bai type: - File - 'null' -- id: hla__fastq - outputSource: process_alignment/hla__fastq - type: - - 'null' - - items: File - type: array - id: work_bam_plus__disc - outputSource: process_alignment/work_bam_plus__disc + outputSource: merge_split_alignments/work_bam_plus__disc secondaryFiles: - .bai type: - File - 'null' - id: work_bam_plus__sr - outputSource: process_alignment/work_bam_plus__sr + outputSource: merge_split_alignments/work_bam_plus__sr secondaryFiles: - .bai type: - File - 'null' +- id: hla__fastq + outputSource: merge_split_alignments/hla__fastq + type: + - 'null' + - items: File + type: array requirements: - class: EnvVarRequirement envDef: @@ -120,3 +121,26 @@ steps: - id: work_bam_plus__disc - id: work_bam_plus__sr run: steps/process_alignment.cwl + scatter: + - process_alignment_rec + scatterMethod: dotproduct +- id: merge_split_alignments + in: + - id: alignment_rec + source: alignment_rec + - id: work_bam + source: process_alignment/work_bam + - id: align_bam_toolinput + source: process_alignment/align_bam + - id: work_bam_plus__disc_toolinput + source: process_alignment/work_bam_plus__disc + - id: work_bam_plus__sr_toolinput + source: process_alignment/work_bam_plus__sr + - id: hla__fastq_toolinput + source: process_alignment/hla__fastq + out: + - id: align_bam + - id: work_bam_plus__disc + - id: work_bam_plus__sr + - id: hla__fastq + run: steps/merge_split_alignments.cwl diff --git a/gvcf_joint/gvcf-joint-workflow/wf-jointcall.cwl b/gvcf_joint/gvcf-joint-workflow/wf-jointcall.cwl index 6aa8c14..3091d1d 100644 --- a/gvcf_joint/gvcf-joint-workflow/wf-jointcall.cwl +++ b/gvcf_joint/gvcf-joint-workflow/wf-jointcall.cwl @@ -49,8 +49,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -62,7 +60,9 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -81,6 +81,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -88,7 +90,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -113,10 +116,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File @@ -196,8 +196,6 @@ outputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -209,7 +207,9 @@ outputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -228,6 +228,8 @@ outputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -235,7 +237,8 @@ outputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -260,10 +263,7 @@ outputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint-workflow/wf-variantcall.cwl b/gvcf_joint/gvcf-joint-workflow/wf-variantcall.cwl index 6c57824..ffabd7e 100644 --- a/gvcf_joint/gvcf-joint-workflow/wf-variantcall.cwl +++ b/gvcf_joint/gvcf-joint-workflow/wf-variantcall.cwl @@ -26,8 +26,6 @@ inputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -39,12 +37,12 @@ inputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double - name: vrn_file type: - 'null' - string - - name: reference__twobit + - name: genome_resources__variation__train_hapmap type: File - name: reference__genome_context type: @@ -64,6 +62,8 @@ inputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -71,7 +71,8 @@ inputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -96,10 +97,7 @@ inputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File @@ -183,8 +181,6 @@ outputs: type: - string - 'null' - - name: genome_resources__variation__train_hapmap - type: File - name: genome_resources__variation__clinvar type: File - name: genome_resources__variation__esp @@ -196,7 +192,9 @@ outputs: - 'null' - string - name: config__algorithm__min_allele_fraction - type: long + type: double + - name: genome_resources__variation__train_hapmap + type: File - name: reference__genome_context type: items: File @@ -215,6 +213,8 @@ outputs: type: string - name: genome_resources__variation__exac type: File + - name: genome_resources__variation__gnomad_exome + type: File - name: genome_resources__aliases__human type: - string @@ -222,7 +222,8 @@ outputs: - boolean - name: config__algorithm__tools_off type: - items: string + - 'null' + - items: 'null' type: array - name: genome_resources__variation__dbsnp type: File @@ -247,10 +248,7 @@ outputs: items: string type: array - name: config__algorithm__effects - type: - - string - - 'null' - - boolean + type: string - name: config__algorithm__variant_regions type: - File diff --git a/gvcf_joint/gvcf-joint.yaml b/gvcf_joint/gvcf-joint.yaml index 5abd5ad..981d8ea 100644 --- a/gvcf_joint/gvcf-joint.yaml +++ b/gvcf_joint/gvcf-joint.yaml @@ -5,12 +5,9 @@ details: trim_reads: read_through adapters: polyx aligner: bwa - align_split_size: false recalibrate: true variantcaller: [gatk-haplotype, strelka2] tools_on: [gvcf] - tools_off: [gemini] - effects: false validate: ../testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf validate_regions: ../testdata/automated/variant_regions-bam.bed variant_regions: ../testdata/automated/variant_regions-bam.bed @@ -23,12 +20,9 @@ details: files: ../testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam - algorithm: aligner: bwa - align_split_size: false recalibrate: true variantcaller: [gatk-haplotype, strelka2] - effects: false tools_on: [gvcf] - tools_off: [gemini] variant_regions: ../testdata/automated/variant_regions-bam.bed metadata: batch: b1