Explore Workflows

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

Graph Name Retrieved From View
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/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 8587882f145d3eb8e258e7bf819a94f8dd666dbf
workflow graph fillout_post_processing.cwl

https://github.com/mskcc/pluto-cwl.git

Path: cwl/fillout_post_processing.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933
workflow graph apolloServer-createOrganism-workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: apolloServer-createOrganism-workflow.cwl

Branch/Commit ID: 556884e8e205295e561b1d9140d836cdd6c1d8c9
workflow graph rhapsody_targeted_1.9-beta.cwl#UncompressDatatables.cwl

https://github.com/longbow0/cwl.git

Path: v1.9-beta/rhapsody_targeted_1.9-beta.cwl

Branch/Commit ID: b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e

Packed ID: UncompressDatatables.cwl
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph genomics-workspace-genome.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl

Branch/Commit ID: 556884e8e205295e561b1d9140d836cdd6c1d8c9
workflow graph Vegetation index

Vegetation index processor, the greatest

 https://github.com/EOEPCA/app-vegetation-index.git

Path: vegetation-index.cwl

Branch/Commit ID: a53413792989b9ed3008b09a74a1580eea440fe5

Packed ID: vegetation-index
workflow graph nested.cwl

https://github.com/giannisdoukas/CWLJNIKernel.git

Path: tests/cwl/nested.cwl

Branch/Commit ID: e07959c147a9a4f5470f5ed3c22e37356ec92197
workflow graph Quality assessment, amplicon classification and functional prediction

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_ngtax_picrust2.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c