Explore Workflows

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: master

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: c211071

https://github.com/genome/cancer-genomics-workflow.git

Path: varscan/germline_workflow.cwl

Branch/Commit ID: toil_compatibility

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl

Branch/Commit ID: master

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/mr-c/datirium-workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: license_test

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

Path: modules/pair/structural-variants-pair.cwl

Branch/Commit ID: master

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/sorter.cwl

Branch/Commit ID: master

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: dev

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/yeolab/eclip.git

Path: cwl/wf_trim_and_map_pe.cwl

Branch/Commit ID: master

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: 3bb03c9b