Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c
workflow graph Trim Galore RNA-Seq pipeline paired-end

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: 2c486543c335bb99b245dfe7e2f033f535efb9cf
workflow graph gaps_or_not.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: gaps_or_not.cwl

Branch/Commit ID: aa375dcaa5ccfbb4e2aa4433d10948c641b044eb
workflow graph io-union-input-default-wf.cwl

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

Path: tests/io-union-input-default-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 4642316a30a95d4f3d135c18f98477886b160094
workflow graph alignment_workflow_md5checker.cwl

https://github.com/DataBiosphere/topmed-workflows.git

Path: aligner/topmed-cwl/workflow/alignment_workflow_md5checker.cwl

Branch/Commit ID: 93ae9307a92abcc40d639592464c4b491818611b
workflow graph scatter-wf4.cwl#main

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

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

Branch/Commit ID: 9e7c68c0834645ba53a7e2b5f70d53df9d051c92

Packed ID: main
workflow graph pass-unconnected.cwl

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

Path: tests/pass-unconnected.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph oxog_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: oxog_sub_wf.cwl

Branch/Commit ID: 40bf56daf9edab82e0f964dbd6961ca1111cd35f
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05