Explore Workflows

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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/rnaseq-pe-dutp.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/marianas/collapsed_fastq_to_bam.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3

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: 12c29f88855329192bfff977f046990031f04931

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

Path: metadata/advanced-header.cwl

Branch/Commit ID: e7a896db41063c52197aec8d5b49ed013d7a5ba7

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines9-wf-noET.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/duplicated_readgroup_fix.cwl

Branch/Commit ID: 286bce04c474d28bddeb7dbe43ab8d59919fe855

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 7319ccfd2108929588bdc266d9df198629dfaa65