Explore Workflows

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

Graph Name Retrieved From View
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: 7eef0294395d83ff0765fce61726a59d71126422
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5
workflow graph count-lines5-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: ae401a813472ca453a99ad067a5e6fc3bd71112b
workflow graph mutect panel-of-normals workflow

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

Path: definitions/pipelines/panel_of_normals.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 0a9a4ce83b49ed4e7eee5bcc09d83725136a36b0
workflow graph Resize sentinel2ard collection

Resize sentinel2ard collection

 https://github.com/EO-DataHub/eodh-training.git

Path: cwl/resize-sentinel2ard.cwl

Branch/Commit ID: a2272a943ecce59c624e5016cc5d3f392c99ceff

Packed ID: resize-sentinel2ard
workflow graph gathered exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/gathered_cle_somatic_exome.cwl

Branch/Commit ID: a93be3183c2218ee50f13ae2675dd1cde563fdbc
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 31aa094dce60cbb176229d6b918bfd5ae09c0390