Explore Workflows

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

Graph Name Retrieved From View
workflow graph kfdrc_qc_wf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_qc_wf.cwl

Branch/Commit ID: d4e818c8b9bf56c83694639aa542bb5c1a174f7d
workflow graph Create Genomic Collection for Bacterial Pipeline

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

Path: genomic_source/wf_genomic_source.cwl

Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77
workflow graph RNA-Seq pipeline paired-end strand specific

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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.cwl

Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726
workflow graph scatter-wf4.cwl#main

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

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94

Packed ID: main
workflow graph scatter-valuefrom-wf2.cwl

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

Path: tests/scatter-valuefrom-wf2.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph Nested workflow example

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

Path: tests/wf/double-nested.cwl

Branch/Commit ID: 6d8c2a41e2c524e8d746020cc91711ecc3418a23
workflow graph project-workflow-sv.cwl

https://github.com/mskcc/argos-cwl.git

Path: project-workflow-sv.cwl

Branch/Commit ID: 7c694b51d9d593439cf8ab3e5006665f0bbe2149
workflow graph Unaligned BAM to BQSR

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass2.cwl

Branch/Commit ID: 1cfd46014be8d867044cb10d1ddde0cb3068ee84