Explore Workflows

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

Graph Name Retrieved From View
workflow graph Feature expression merge - combines feature expression from several experiments

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

https://github.com/datirium/workflows.git

Path: workflows/feature-merge.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4
workflow graph io-file-default-wf.cwl

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/io-file-default-wf.cwl

Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9
workflow graph Seed Protein Alignments I

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

Path: protein_alignment/wf_seed_1.cwl

Branch/Commit ID: 803f6367d1b279a7b6dc1a4e8ae43f1bbec9f760
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: 803f6367d1b279a7b6dc1a4e8ae43f1bbec9f760
workflow graph Filter Protein Alignments I

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 803f6367d1b279a7b6dc1a4e8ae43f1bbec9f760
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1
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: aebf2355539fdf81fd9082616f8b21440d2691c6