Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 295e7b7f51727c0f2d6cc86ce817449b2e8dba3c
workflow graph samtools_view_sam2bam

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

Path: structuralvariants/subworkflows/samtools_view_sam2bam.cwl

Branch/Commit ID: 70eec658fd1b92c4d0e3b24146820010b5983d41
workflow graph testTimeSIMLR.cwl

https://github.com/Gepiro/rCASCStreamFlow.git

Path: setting/testTimeSIMLR.cwl

Branch/Commit ID: 130d399d0fbbbd65042d103176be67d7952ba003
workflow graph SSU-from-tablehits.cwl

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 316831663e84623eb0e3a260af252fef441924d4
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/wgs_alignment.cwl

Branch/Commit ID: e649fcb1092905c539be026a3f23c82d5b0871d2
workflow graph rnaseq-alignment-quantification

This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/RNA-Seq/rnaseq-quantification-qc.cwl

Branch/Commit ID: 3b9736a19eed3efc8f6cc587df282aad4f50a2ee
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: 730b40bc403263b724399a952c0f3e2d28f13519
workflow graph bwa_index

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

Path: structuralvariants/subworkflows/bwa_index.cwl

Branch/Commit ID: 70eec658fd1b92c4d0e3b24146820010b5983d41
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: e649fcb1092905c539be026a3f23c82d5b0871d2
workflow graph allele-process-strain.cwl

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b