Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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strelka workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/strelka_and_post_processing.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
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cnv_manta
CNV Manta calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/cnv_manta.cwl Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c |
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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: 0805e8e0d358136468e0a9f49e06005e41965adc |
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Cell Ranger ARC Count Gene Expression + ATAC
Cell Ranger ARC Count Gene Expression + ATAC ============================================ |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-arc-count.cwl Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86 |
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taxonomy_check_16S
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https://github.com/ncbi/pgap.git
Path: task_types/tt_taxonomy_check_16S.cwl Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3 |
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Raw sequence data to BQSR
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_bqsr.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
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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: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a |
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samtools_sort
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c |
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sequence (bam or fastqs) to trimmed fastqs and HISAT alignments
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370 |
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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: 935a78f1aff757f977de4e3672aefead3b23606b |
