Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

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

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/align_and_count.cwl

Branch/Commit ID: 0a8c54b014101112fa4a2cb5fce5c30133691cae
workflow graph upload2ebi.workflow.cwl

https://github.com/MG-RAST/ebi-submitter.git

Path: CWL/workflows/upload2ebi.workflow.cwl

Branch/Commit ID: 98fd007564f473fd9d720e4e67ebf7bdde3ab58a
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a
workflow graph bqsr_workflow.cwl

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

Path: workflows/BQSR/bqsr_workflow.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf