Explore Workflows
View already parsed workflows here or click here to add your own
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star-cufflinks_wf_pe.cwl
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https://github.com/pitagora-network/pitagora-cwl.git
Path: workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.cwl Branch/Commit ID: f85f2cd5d888ed947f47a391eb32dcb53265f9b3 |
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Interval overlapping alignments counts
Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals. |
https://github.com/datirium/workflows.git
Path: workflows/bedtools-multicov.cwl Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c |
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Cellranger Reanalyze
Cellranger Reanalyze ==================== |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-reanalyze.cwl Branch/Commit ID: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb |
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Varscan Workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan_germline.cwl Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5 |
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hisat2-stringtie_wf_pe.cwl
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https://github.com/pitagora-network/pitagora-cwl.git
Path: workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.cwl Branch/Commit ID: f85f2cd5d888ed947f47a391eb32dcb53265f9b3 |
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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: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb |
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GATK4_SomaticVariantCaller_4_1_3_0.cwl
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https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git
Path: janis_pipelines/wgs_somatic/cwl/tools/GATK4_SomaticVariantCaller_4_1_3_0.cwl Branch/Commit ID: 5ba65e4781f03a74a845b7cd40bbf4c2ae3a9844 |
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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: 8438316338e66823e1c9aca9f675b2bf33f2aa59 |
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heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
https://github.com/Barski-lab/workflows.git
Path: tools/heatmap-prepare.cwl Branch/Commit ID: 2ffe30af333aead4f2a7e181ab151587e825b384 |
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gathered exome alignment and somatic variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_exome_gathered.cwl Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5 |
