Explore Workflows

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

Graph Name Retrieved From View
workflow graph msi.cwl

https://github.com/mskcc/innovation-pipeline.git

Path: workflows/subworkflows/msi.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de
workflow graph fastq_foreign_chromosome_cleanup

This workflow remove foreign chromosome contamination by taxonomic groups

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Contamination/fastq-foreign-chromosome-cleanup_test.cwl

Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph WGS and MT analysis for fastq files

rna / protein - qc, preprocess, filter, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/wgs-fastq.workflow.cwl

Branch/Commit ID: 1844de830f6935901849ccd9966685fbf13e8042
workflow graph rnaseq-pe-dutp-mitochondrial.cwl

RNA-Seq strand specific mitochondrial workflow for pair-end experiment based on original BioWardrobe's basic analysis.

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

Path: workflows/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph 02-local-compare-across-alg.cwl

https://github.com/PNNL-CompBio/decomprolute.git

Path: localData/02-local-compare-across-alg.cwl

Branch/Commit ID: 6351764c74a44fc4fa2042d31c0cedde5a5bdbe9
workflow graph Create Genomic Collection for Bacterial Pipeline

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

Path: genomic_source/wf_genomic_source.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph gather AML trio outputs

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

Path: definitions/pipelines/aml_trio_cle_gathered.cwl

Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
workflow graph count-lines2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9
workflow graph RNA-Seq pipeline single-read 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 single-read** 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 single-read 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-se-dutp-mitochondrial.cwl

Branch/Commit ID: c5bae2ca862c764911b83d1f15ff6af4e2a0db28