Explore Workflows

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

Graph Name Retrieved From View
workflow graph iwdr_with_nested_dirs.cwl

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: bf93dd3e6e3261e1455530984ce045f283535d17
workflow graph mutect panel-of-normals workflow

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

Path: definitions/pipelines/panel_of_normals.cwl

Branch/Commit ID: 67f56d3b9c70ad56019ed8aa8d50a128e02be43b
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph bulk_analysis.cwl

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

Path: steps/bulk_analysis.cwl

Branch/Commit ID: 00c5e3ad729c1712945c69b58bd9868115d11bfd
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

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 pair-end** 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 the pair-end 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-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
workflow graph indices-header.cwl

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

Path: metadata/indices-header.cwl

Branch/Commit ID: fc6f4183b941dcf616a9146fbb369a9af0683849
workflow graph allele-process-reference.cwl

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

Path: subworkflows/allele-process-reference.cwl

Branch/Commit ID: d47fdb25c56124dadd33b05a90273f64064d69e4
workflow graph Single-cell Reference Indices

Single-cell Reference Indices Builds a Cell Ranger and Cell Ranger ARC compatible reference folders from the custom genome FASTA and gene GTF annotation files

 https://github.com/Barski-lab/sc-seq-analysis.git

Path: workflows/sc-ref-indices-wf.cwl

Branch/Commit ID: d82c558f4bf32d41fdae0251c48baf8cef7de32e
workflow graph cluster_blastp_wnode and gpx_qdump combined

https://github.com/ncbi/pgap.git

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e