Explore Workflows

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

Graph Name Retrieved From View
workflow graph step-valuefrom5-wf.cwl

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

Path: tests/step-valuefrom5-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph checkm

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

Path: checkm/wf_checkm.cwl

Branch/Commit ID: 8af4e2aabf43d5e3c7162efae4ad4649df5601e2
workflow graph bwa_index

Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl

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

Path: structuralvariants/cwl/subworkflows/bwa_index.cwl

Branch/Commit ID: 6ccec9c5c5bc9fb4e75ca0b9cc22d13df9ffb815
workflow graph concatenate-flag.cwl

https://git.astron.nl/RD/VLBI-cwl.git

Path: workflows/concatenate-flag.cwl

Branch/Commit ID: 63666fe1bf33f3dd2c9e156cfc28e45ad3945ca8
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca
workflow graph optional_src_mandatory_sink.cwl

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

Path: tests/wf/optional_src_mandatory_sink.cwl

Branch/Commit ID: dbc4c4c2ad30ed31367b4fbcc3bb4084fdcabaa2
workflow graph scatter-valuefrom-inputs-wf1.cwl

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

Path: tests/scatter-valuefrom-inputs-wf1.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
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: ebbf23764ede324cabc064bd50647c1f643726fa