Explore Workflows

https://github.com/bespin-workflows/exomeseq-gatk4.git

Path: subworkflows/exomeseq-gatk4-00-prepare-reference-data.cwl

Branch/Commit ID: develop

https://github.com/idaks/cwl_modeling.git

Path: yw_cwl_modeling/yw2cwl_parser/example_sql/Sentiment_NLTK/wf_Sentiment_NLTK.cwl

Branch/Commit ID: master

https://github.com/kinow/pipeline-v5.git

Path: workflows/conditionals/qc.cwl

Branch/Commit ID: eosc-life-gos

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/validate_interleaved_fq.cwl

Branch/Commit ID: 0.5.0

https://github.com/hubmapconsortium/sprm.git

Path: pipeline.cwl

Branch/Commit ID: d42d6f5

https://github.com/pjotrp/CWL-workflows.git

Path: Workflows/test-workflow.cwl

Branch/Commit ID: guix-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/mr-c/datirium-workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: license_test

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

Path: cwl/wf_get_peaks_nostats_se.cwl

Branch/Commit ID: master

https://github.com/nigyta/rice_reseq.git

Path: workflows/fastq2bam.cwl

Branch/Commit ID: master

This workflow essentially restructures the inputs before sending to wf_full_IDR_pipeline_1input.cwl

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

Path: cwl/wf_full_IDR_pipeline_1input_sample.cwl

Branch/Commit ID: master