Explore Workflows
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Graph | Name | Retrieved From | View |
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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: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9 |
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cond-wf-004.1.cwl
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![]() Path: testdata/cond-wf-004.1.cwl Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51 |
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wf-loadContents3.cwl
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![]() Path: tests/wf-loadContents3.cwl Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3 |
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env-wf1.cwl
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![]() Path: tests/env-wf1.cwl Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3 |
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steplevel-resreq.cwl
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![]() Path: cwltool/schemas/v1.0/v1.0/steplevel-resreq.cwl Branch/Commit ID: 20d664eff23e59aa57908345bfdb1ceeab3438f2 |
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Motif Finding with HOMER with custom background regions
Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/) |
![]() Path: workflows/homer-motif-analysis-bg.cwl Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b |
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revsort-array.cwl
Reverse the lines in a document, then sort those lines. |
![]() Path: input-data/revsort-array.cwl Branch/Commit ID: 4fd8e7dbcff5492cb32e4fb15263a51fa4490cf1 |
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Varscan Workflow
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![]() Path: definitions/subworkflows/varscan_germline.cwl Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c |
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exome alignment with qc, no bqsr, no verify_bam_id
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![]() Path: definitions/pipelines/alignment_exome_nonhuman.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec |
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RNA-seq alelle specific pipeline for paired-end data
Allele specific RNA-Seq paired-end workflow |
![]() Path: workflows/allele-rnaseq-pe.cwl Branch/Commit ID: c602e3cdd72ff904dd54d46ba2b5146eb1c57022 |