Explore Workflows
View already parsed workflows here or click here to add your own
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foreign_screening.cwl
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https://github.com/ncbi/pgap.git
Path: vecscreen/foreign_screening.cwl Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b |
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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: 799575ce58746813f066a665adeacdda252d8cab |
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Run pindel on provided region
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: 8eb189a4a34dc8cd86380685f814c79a444a7601 |
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wf_demultiplex_se.cwl
This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol) |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_demultiplex_se.cwl Branch/Commit ID: 7196b92e262fe5f8acee04cb0d1b6fd23e4febdc |
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tt_fscr_calls_pass1
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https://github.com/ncbi/pgap.git
Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b |
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wgs alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_wgs.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec |
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Detect Docm variants
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/docm_cle.cwl Branch/Commit ID: 8eb189a4a34dc8cd86380685f814c79a444a7601 |
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umi molecular alignment workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: 8eb189a4a34dc8cd86380685f814c79a444a7601 |
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fp_filter workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/fp_filter.cwl Branch/Commit ID: 10870aefd20469e728969269ff3c54b3b8339a18 |
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bgzip and index VCF
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bgzip_and_index.cwl Branch/Commit ID: 8eb189a4a34dc8cd86380685f814c79a444a7601 |
