Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph 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/datirium/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 472d453995dcda1b66884c31db562f4fb6094e5a
workflow graph main.cwl

https://github.com/alpha-unito/cwl-1000genome-workflow.git

Path: main.cwl

Branch/Commit ID: 77aaa24c2576826a9a11380b70e84507a53081e8
workflow graph count-lines7-wf_v1_1.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: 139c64b55f7693d22e6646b8afe585f90da11dcb
workflow graph STAR-Alignment-PE

This workflow aligns the fastq files using STAR for paired-end samples

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Alignments/star-alignment.cwl

Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/exome_alignment_mouse.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc
workflow graph preprocess_vcf.cwl

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git

Path: preprocess_vcf.cwl

Branch/Commit ID: b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb
workflow graph annotator_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git

Path: annotator_sub_wf.cwl

Branch/Commit ID: b4a02b7ba5733b3cc5b84b79ab0634ff9e4d1aeb
workflow graph analysis-workflow.cwl

https://github.com/mskcc/pluto-cwl.git

Path: cwl/analysis-workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933
workflow graph md_launch_mutate.cwl

https://github.com/douglowe/biobb_hpc_cwl_md_list.git

Path: md_launch_mutate.cwl

Branch/Commit ID: 97122f21048a5ac4a12b21059b751d1d07050cbd
workflow graph qa_check_subwf.cwl

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: qa_check_subwf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3