Explore Workflows

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

Graph Name Retrieved From View
workflow graph indices-header.cwl

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

Path: metadata/indices-header.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph bam_filtering

BAM filtering

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

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c
workflow graph env-wf2.cwl

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

Path: tests/env-wf2.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants_mouse.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
workflow graph scatter-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c
workflow graph scatter-valuefrom-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389
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: 7eef0294395d83ff0765fce61726a59d71126422
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph count-lines13-wf.cwl

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

Path: v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad
workflow graph extract_amplicon_kit.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_amplicon_kit.cwl

Branch/Commit ID: 6b43e8b03256492f2b36ffcf548704daaafee6f6