Explore Workflows

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

Path: tests/scatter-wf3.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3

Packed ID: main

https://github.com/sfu-ireceptor/airr-seqaa.git

Path: cwl/id_to_json_workflow.cwl

Branch/Commit ID: 3fa8eb2ccbd64e1e9731aa431156178077080f61

BAM filtering

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

Path: structuralvariants/subworkflows/bam_filtering.cwl

Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e

This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/standard_pipeline.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b

Packed ID: main

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

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

Branch/Commit ID: ec73c7be10c97ebd39e3f87ac3601fff58e24d3f

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

Path: cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl

Branch/Commit ID: 227f35a5ed50c423afba2353871950aa61d58872

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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 file 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/rnaseq-se-dutp-mitochondrial.cwl

Branch/Commit ID: 1a46cb0e8f973481fe5ae3ae6188a41622c8532e

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 3f85843d4a6debdabe96bc800bf2a4efdcda1ef3

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

Path: tests/record-in-secondaryFiles-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b