Explore Workflows

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

Graph Name Retrieved From View
workflow graph Compute average of average per cross-mapped famil(y)ies

Compute average structure for all averaged structures corresponding to UniProt domain instances cross-mapped from Pfam/CATH to a CATH/Pfam family. First computes average per UniProt domain instance and then average all averaged structures per Pfam family.

https://github.com/HrishiDhondge/CroMaSt.git

Path: Tools/other_avg_subwf.cwl

Branch/Commit ID: b5a9d4b025ec8e065bae97eeb96f10db2dd8e1e6
workflow graph HLA LA workflow

https://github.com/mdaya/hla_la_typing.git

Path: HLA_LA_workflow.cwl

Branch/Commit ID: f6d1debfd7fcaf203a38aad7ff57f689c2cbbbfd
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: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
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/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 801f7b363e0599b9a28ecda696dfdb1c0e40ce71
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb
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: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph CroMaSt.cwl

https://github.com/HrishiDhondge/CroMaSt.git

Path: CroMaSt.cwl

Branch/Commit ID: b5a9d4b025ec8e065bae97eeb96f10db2dd8e1e6
workflow graph clipAteam.cwl

https://github.com/lonbar/VLBI-cwl.git

Path: workflows/clipAteam.cwl

Branch/Commit ID: 58d6c7fe14e9a4de4e1659f8eedd2ca527c18a28
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Long-covid.cwl

https://github.com/cwlviewer-test/Long-covid---aedea650-7a21-11ed-b9d2-e51f21933d80.git

Path: Long-covid.cwl

Branch/Commit ID: e6e351cba4bf23073daa00364da5290d3c87738e