Explore Workflows

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

Graph Name Retrieved From View
workflow graph samtools_sort

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

Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl

Branch/Commit ID: 93fbc4e51770d953fc44104a7b09436f75719470
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/exome.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph 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 **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.cwl

Branch/Commit ID: a839eb6390974089e1a558c49fc07b4c66c50767
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: efb40a812cdba2df6699f130ee5aeea9b63045cd
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph sum-wf.cwl

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

Path: tests/sum-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph RNA-Seq pipeline single-read

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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.cwl

Branch/Commit ID: 44214a9d02e6d85b03eb708552ed812ae3d4a733
workflow graph find_hotspots_in_normals.cwl

Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/subworkflows/find_hotspots_in_normals.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph find_hotspots_in_normals.cwl

Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups

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

Path: workflows/subworkflows/find_hotspots_in_normals.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf