Explore Workflows

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

Graph Name Retrieved From View
workflow graph download_pheno.cwl

https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess.git

Path: cwl/workflows/download_pheno.cwl

Branch/Commit ID: 9724eed7d80cc1a4273b38f5b9cd2526d1579a29
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: d1bef74924efcb8bfaa00987b3f148d5a192b7a9
workflow graph scRNA-seq pipeline using Salmon and Alevin

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: pipeline.cwl

Branch/Commit ID: a5779cc2804edf3052e597ea32f1f1c49aa33afb
workflow graph bgzip and index VCF

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: 3bb0693076adc1543079a6b136c74906ad546ac6
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 2229f26ec424f9ebeb3db7fec3bd3f84a38c7485
workflow graph Run genomic CMsearch (5S rRNA)

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: dcbbce152fbff2637f102471fb80318244492853
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

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

Path: wf_common.cwl

Branch/Commit ID: 2229f26ec424f9ebeb3db7fec3bd3f84a38c7485
workflow graph kallisto_wf_se.cwl

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/kallisto/single_end/kallisto_wf_se.cwl

Branch/Commit ID: a7594ee9c8b969c8f39a166753372d31ee68edcf
workflow graph bgzip and index VCF

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: eb0092603bf57acb7bda08a06e4f2f1e2a8c9b6d