Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph wf_full_IDR_pipeline_1input_scatter.cwl

The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_full_IDR_pipeline_1input_scatter.cwl

Branch/Commit ID: aedc0a14d4ba109ee65678a3201a52c5bb6ad473
workflow graph tt_blastn_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: f2bd4687f06f85ea848b6f1ce04ec97f48525334
workflow graph Hello World

Outputs a message using echo

 https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/hello-workflow.cwl

Branch/Commit ID: 9f3b9e7b74d5a904b12674dfd1300b56a48c3d33
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
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: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c
workflow graph ChIP-seq peak caller workflow MACS2 based

This workflow execute peak caller and QC for ChIP-seq using MACS2

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

Path: workflows/ChIP-Seq/peak-calling-MACS2.cwl

Branch/Commit ID: e541470bc9d0b064bc4ed7dd2b45d8ec67760613
workflow graph Hello World

Outputs a message using echo

 https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/hello-workflow.cwl

Branch/Commit ID: 78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf
workflow graph bacterial_kmer

https://github.com/ncbi/pgap.git

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph Filter Protein Alignments

https://github.com/ncbi/pgap.git

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49