Explore Workflows

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Graph	Name	Retrieved From	View
	mutect panel-of-normals workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/panel_of_normals.cwl Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
	exome alignment with qc, no bqsr, no verify_bam_id	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_exome_nonhuman.cwl Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
	fillout_index_prefilter.cwl	https://github.com/mskcc/pluto-cwl.git Path: cwl/fillout_index_prefilter.cwl Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153
	bam-bedgraph-bigwig.cwl Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.	https://github.com/Barski-lab/workflows.git Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d
	RNA-Seq alignment and transcript/gene abundance workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/rnaseq.cwl Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
	wf-loadContents3.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/wf-loadContents3.cwl Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
	wffail.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/wffail.cwl Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883
	workflow.cwl CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files Inputs ------ The following parameters are required: project_id project_pi request_pi project_short_name project_name project_description cancer_type cancer_study_identifier argos_version_string helix_filter_version is_impact extra_pi_groups The following filenames are required: analysis_mutations_filename analysis_gene_cna_filename analysis_sv_filename analysis_segment_cna_filename cbio_segment_data_filename cbio_meta_cna_segments_filename The following filenames have default values and are optional: cbio_mutation_data_filename cbio_cna_data_filename cbio_fusion_data_filename cbio_clinical_patient_data_filename cbio_clinical_sample_data_filename cbio_clinical_sample_meta_filename cbio_clinical_patient_meta_filename cbio_meta_study_filename cbio_meta_cna_filename cbio_meta_fusions_filename cbio_meta_mutations_filename cbio_cases_all_filename cbio_cases_cnaseq_filename cbio_cases_cna_filename cbio_cases_sequenced_filename Output ------ Workflow output should look like this: output ├── analysis │ ├── <project_id>.gene.cna.txt │ ├── <project_id>.muts.maf │ ├── <project_id>.seg.cna.txt │ └── <project_id>.svs.maf └── portal ├── case_list │ ├── cases_all.txt │ ├── cases_cnaseq.txt │ ├── cases_cna.txt │ └── cases_sequenced.txt ├── data_clinical_patient.txt ├── data_clinical_sample.txt ├── data_CNA.ascna.txt ├── data_CNA.scna.txt ├── data_CNA.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_fusions.txt ├── meta_mutations_extended.txt ├── meta_study.txt ├── <project_id>_data_cna_hg19.seg └── <project_id>_meta_cna_hg19_seg.txt	https://github.com/mskcc/pluto-cwl.git Path: cwl/workflow.cwl Branch/Commit ID: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e
	Subworkflow that runs cnvkit in single sample mode and returns a vcf file	https://github.com/apaul7/cancer-genomics-workflow.git Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
	joint genotyping for trios or small cohorts	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/joint_genotype.cwl Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea