Explore Workflows

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

https://github.com/datirium/workflows.git

Path: workflows/genome-indices.cwl

Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 441b85003fdc10cf4cbf333d89acb4d23b0fef32

Workflow to run GetBaseCountsMultiSample fillout on a number of bam files with a single maf file

https://github.com/mskcc/pluto-cwl.git

Path: cwl/fillout_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl

Branch/Commit ID: 3e9bca4e006eae7e9febd76eb9b8292702eba2cb

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

https://github.com/datirium/workflows.git

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: 12c29f88855329192bfff977f046990031f04931

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

https://github.com/datirium/workflows.git

Path: workflows/trim-rnaseq-pe.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 1bf7dc7b03ea3c64e54375cc5c3767849a801000

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/conpair/0.2/conpair-master.cwl

Branch/Commit ID: b5ce620cd29416412181929a83695286786c4e7b

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141