Explore Workflows

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

Graph Name Retrieved From View
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: 18b8fdf7d425d8e7d8986e08904ef09492798cf6
workflow graph helloworld-slurmcern.cwl

https://github.com/reanahub/reana-demo-helloworld.git

Path: workflow/cwl/helloworld-slurmcern.cwl

Branch/Commit ID: 75f3e615171308b85495e593a35fbb64e27bf5d3
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5
workflow graph Trim Galore 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 **pair-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe.cwl

Branch/Commit ID: b957a4f681bf0ca8ebba4e0d0ec3936bf79620c5
workflow graph bacterial_kmer

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 9144d08fa7f4e852498761481dceab477167fa65
workflow graph Downsample and HaplotypeCaller

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

Path: definitions/pipelines/downsample_and_recall.cwl

Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 49508a2757ff2f49f1c200774a38af1c12b531bf
workflow graph run-one.cwl

https://github.com/hubmapconsortium/hra-workflows.git

Path: steps/run-one.cwl

Branch/Commit ID: 118a0e83052b6edfb72dd46bab8828314a0db34c
workflow graph protein annotation

Proteins - predict, filter, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-filter-annotation.workflow.cwl

Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f
workflow graph preprocess fasta

Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/preprocess-fasta.workflow.cwl

Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f