Explore Workflows

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

Graph Name Retrieved From View
workflow graph waltz-workflow.cwl

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

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: daba08457dd53fb81d11acb274c29a77b6122316
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 8d8512061f2367c90aac67bcbf92af1061b4af59

Packed ID: main
workflow graph Produce a list of residue-mapped structural domain instances from Pfam ids

Retrieve and process the PDB structures corresponding to the Pfam family ids resulting in a list of residue-mapped structural domain instances along with lost structural instances (requires Data/pdbmap downloaded from Pfam and uses SIFTS resource for UniProt to PDB residue Mapping)

https://gitlab.inria.fr/capsid.public_codes/CroMaSt.git

Path: Tools/resmapping_pfam_instances_subwf.cwl

Branch/Commit ID: 9f3832867eab6c7a6363f8ca594a4bcf2ff7e96f
workflow graph record-in-secondaryFiles-missing-wf.cwl

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

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

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html Modified 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-smarter-dutp.cwl

Branch/Commit ID: 92f1a6da9c4f85fb51340b01b32373a50fde0891
workflow graph module-1.cwl

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

Path: workflows/module-1.cwl

Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0
workflow graph qiime2 rarefaction visualization

Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/bespin-workflows/16s-qiime2.git

Path: subworkflows/qiime2-07-alpha-rarefaction.cwl

Branch/Commit ID: b4c07a7e07ba9ce862a2be057a905d300f3c8882
workflow graph call_variants.cwl

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

Path: workflows/subworkflows/call_variants.cwl

Branch/Commit ID: 5bf88423593441e4bf6b432111160446cd8dcf13
workflow graph qc_workflow.cwl

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

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f