Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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bam_qc_stats
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https://github.com/msk-access/qc_generation.git
Path: access_qc__packed.cwl Branch/Commit ID: develop Packed ID: bam_qc_stats.cwl |
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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/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: master |
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03-map-pe-umis.cwl
STARR-seq 03 mapping - reads: PE |
https://github.com/alexbarrera/GGR-cwl.git
Path: v1.0/STARR-seq_pipeline/03-map-pe-umis.cwl Branch/Commit ID: master |
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EMG pipeline v3.0 (paired end version)
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/emg-pipeline-v3-paired.cwl Branch/Commit ID: a8abd0e |
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compile1.cwl#main
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https://github.com/common-workflow-language/workflows.git
Path: workflows/compile/compile1.cwl Branch/Commit ID: master Packed ID: main |
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qiime2 create phylogenetic tree
Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
https://github.com/Duke-GCB/bespin-cwl.git
Path: packed/qiime2-step2-dada2.cwl Branch/Commit ID: qiime2-workflow Packed ID: qiime2-05-phylogeny.cwl |
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rhapsody_targeted_1.9-beta.cwl#VDJ_tcr.cwl
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https://github.com/longbow0/cwl.git
Path: v1.9-beta/rhapsody_targeted_1.9-beta.cwl Branch/Commit ID: master Packed ID: VDJ_tcr.cwl |
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alignment_workflow_md5checker.cwl
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https://github.com/databiosphere/topmed-workflows.git
Path: aligner/topmed-cwl/workflow/alignment_workflow_md5checker.cwl Branch/Commit ID: 1.32.0 |
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SSU-from-tablehits.cwl
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 3f85843 |
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basic.cwl
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https://github.com/ljdursi/cwl-tutorial.git
Path: cl-tools/workflow/basic.cwl Branch/Commit ID: master |