Explore Workflows

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

Graph Name Retrieved From View
workflow graph Bisulfite alignment and QC

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph DESeq - differential gene expression analysis

Differential gene expression analysis based on the negative binomial distribution

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

Path: workflows/deseq.cwl

Branch/Commit ID: 9a2c389364674221fab3f0f6afdda799e6aa3247
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph bulk_analysis.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_analysis.cwl

Branch/Commit ID: 53415520f94ac0d9a1fae89af0f6e8250240723a
workflow graph exomeseq-00-prepare-reference-data.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-00-prepare-reference-data.cwl

Branch/Commit ID: 9f96a6621a0925d4a1ef4b6a733316149520b008
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

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-dutp.cwl

Branch/Commit ID: 4ab9399a4777610a579ea2c259b9356f27641dcc
workflow graph count-lines18-wf.cwl

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

Path: tests/count-lines18-wf.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
workflow graph merge and annotate svs with population allele freq and vep

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/umi_molecular_alignment.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph timelimit2-wf.cwl

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

Path: tests/timelimit2-wf.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3