Explore Workflows

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: d76110e0bfc40c874f82e37cef6451d74df4f908

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

Path: definitions/subworkflows/joint_genotype.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

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

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-valuefrom-wf3.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

Packed ID: main

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines16-wf.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/timelimit-wf.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_target/prep.cwl

Branch/Commit ID: 7b6185e2e6f9d36b1987274e82842c82ba6f8342

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 1cfd46014be8d867044cb10d1ddde0cb3068ee84

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: cf84038de256c7ca98657ad81734d1aca1dad8c1