Explore Workflows
View already parsed workflows here or click here to add your own
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Chunked version of phmmer-v3.2.cwl
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https://github.com/mscheremetjew/workflow-is-cwl.git
Path: workflows/phmmer-v3.2-chunked-wf.cwl Branch/Commit ID: master |
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Dockstore.cwl
updated description testing 1.9.2 |
https://github.com/NatalieEO/ghapps-single-workflow.git
Path: Dockstore.cwl Branch/Commit ID: master |
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count-lines10-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines10-wf.cwl Branch/Commit ID: main |
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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/mr-c/datirium-workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: license_test |
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Transcripts annotation workflow
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https://github.com/EBI-Metagenomics/workflow-is-cwl.git
Path: workflows/TranscriptsAnnotation-wf.cwl Branch/Commit ID: assembly |
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pack.cwl
create textures and pack them to be a stellaris mod |
https://gitlab.com/unduthegun/stellaris-emblem-lab.git
Path: pack/pack.cwl Branch/Commit ID: cwl |
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oxog_varbam_annotate_wf.cwl
This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json ` |
https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git
Path: oxog_varbam_annotate_wf.cwl Branch/Commit ID: master |
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chksum_for_a_corrupted_xam_file.cwl
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https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_for_a_corrupted_xam_file.cwl Branch/Commit ID: develop |
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EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/emg-qc-paired.cwl Branch/Commit ID: 56dafa4 |
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Create Genomic Collection for Bacterial Pipeline
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https://github.com/slottad/pgap.git
Path: genomic_source/wf_genomic_source.cwl Branch/Commit ID: master |
