Explore Workflows

Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/bwa_index.cwl

Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/wf-loadContents4.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-phmmer-blast.cwl

Branch/Commit ID: 2f0826a8a5f4f1e98fb5c22bb8f982351d3a159b

Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

https://github.com/Barski-lab/workflows.git

Path: workflows/heatmap.cwl

Branch/Commit ID: b4b7b2e7e508be5eac639f9e323d141daf714c0d

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-chipseq-pe.cwl

Branch/Commit ID: b4b7b2e7e508be5eac639f9e323d141daf714c0d

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

Path: testdata/js-expr-req-wf.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1

Packed ID: wf

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/split_bam_subpipeline.cwl

Branch/Commit ID: f7f887b84734a932534ed6a4732a48852e6169d4

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.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: d7481d03fa4b5b4630392540f598acfb100b421d

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de