Explore Workflows

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

Graph Name Retrieved From View
workflow graph sequence (bam or fastqs) to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 2c7879b47890b9300ab9b5ebd35e17372e077757
workflow graph SV filtering workflow

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

Path: definitions/subworkflows/filter_sv_vcf.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
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: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d
workflow graph sorter.cwl

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

Path: steps/sorter.cwl

Branch/Commit ID: e7f46046a7338b6a2bb914e263278ea9c0207326
workflow graph adapter for sequence_align_and_tag

Some workflow engines won't stage files in our nested structure, so parse it out here

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

Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph SSU-from-tablehits.cwl

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 2104dc36c775de93de3fef77e7f82a19da76b6e3
workflow graph segmentation.cwl

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

Path: steps/segmentation.cwl

Branch/Commit ID: e7f46046a7338b6a2bb914e263278ea9c0207326
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: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph trim-rnaseq-se-dutp.cwl

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

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

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

Branch/Commit ID: 801f7b363e0599b9a28ecda696dfdb1c0e40ce71