Explore Workflows
View already parsed workflows here or click here to add your own
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Build Bismark indices
Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input. |
Path: workflows/bismark-index.cwl Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f |
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scatter-valuefrom-wf4.cwl#main
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Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl Branch/Commit ID: 526f36f93655bfb098f766ff020708b5a707513a Packed ID: main |
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umi duplex alignment fastq workflow
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Path: definitions/pipelines/alignment_umi_duplex.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec |
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igv-report_maf_workflow.cwl
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files |
Path: cwl/igv-report_maf_workflow.cwl Branch/Commit ID: 9f7b5b5f985727a2df34ae86586c296ce757004c |
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count-lines11-wf.cwl
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Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl Branch/Commit ID: ec2cf2da6c31ffedf827a0fb213b5204e172f510 |
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exome alignment and germline variant detection
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Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb |
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count-lines2-wf.cwl
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Path: tests/count-lines2-wf.cwl Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3 |
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count-lines11-wf.cwl
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Path: tests/count-lines11-wf.cwl Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b |
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Generate genome indices for STAR & bowtie
Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files |
Path: workflows/genome-indices.cwl Branch/Commit ID: e99e80a2c19682d59947bde04a892d7b6d90091c |
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Detect Variants workflow for WGS pipeline
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Path: definitions/pipelines/detect_variants_wgs.cwl Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735 |
