Explore Workflows

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

Graph Name Retrieved From View
workflow graph cond-wf-003.1_nojs.cwl

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

Path: tests/conditionals/cond-wf-003.1_nojs.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

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

multiple mzml files, all with the same condition

https://github.com/zmahnoor14/MAW.git

Path: cwl/maw.cwl

Branch/Commit ID: 3d140d4bc4c2aa4d617246ef09a66bf87e383a5a
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de

Packed ID: main
workflow graph gatk4.2.4.1_mutect2_workflow.cwl

GATK4.2.4.1 Mutect2 workflow

https://github.com/NCI-GDC/gatk4_mutect2_cwl.git

Path: subworkflows/gatk4.2.4.1_mutect2_workflow.cwl

Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599
workflow graph count-lines1-wf.cwl

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

Path: tests/count-lines1-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
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: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph exome alignment with qc

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

Path: definitions/pipelines/exome_alignment.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94
workflow graph gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: gatk4-mutect2-tumor-only-cwl/gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl

Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b