Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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nanopore_bcr_abl_umi_analysis.cwl
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https://github.com/teoloup/nanopore_fusion.git
Path: nanopore_bcr_abl_umi_analysis.cwl Branch/Commit ID: 9bbba11454dd9f3a977797149026088eddd5c41f |
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scatter-valuefrom-wf5.cwl
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https://github.com/common-workflow-language/common-workflow-language.git
Path: v1.0/v1.0/scatter-valuefrom-wf5.cwl Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e |
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bam to trimmed fastqs and biscuit alignments
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2 |
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bact_get_kmer_reference
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https://github.com/ncbi/pgap.git
Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 909f26beaf96c2cdfe208f87ecd1e9c3de20b81c |
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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/Barski-lab/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: a8909e86f5bcb048d136f9a7d70b4b6f8f4e485f |
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count-lines10-wf.cwl
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https://github.com/common-workflow-language/common-workflow-language.git
Path: v1.0/v1.0/count-lines10-wf.cwl Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e |
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Salmon quantification, FASTQ -> H5AD count matrix
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https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git
Path: salmon-rnaseq/steps/salmon-quantification.cwl Branch/Commit ID: c338cd390c994eb3601cc7749878add1056953ba |
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sc_atac_seq_process_and_analyze.cwl
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https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git
Path: steps/sc_atac_seq_process_and_analyze.cwl Branch/Commit ID: 7fed36f1bd63d7a3479135473b21fa4c501519a1 |
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snapanalysis_setup_and_analyze.cwl
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https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git
Path: steps/snapanalysis_setup_and_analyze.cwl Branch/Commit ID: 44dbe381f68878ab607b167b62267c4ea97f3322 |
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sc_atac_seq_prep_process_init.cwl
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https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git
Path: sc-atac-seq-pipeline/steps/sc_atac_seq_prep_process_init.cwl Branch/Commit ID: c338cd390c994eb3601cc7749878add1056953ba |
