Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: 6b365b79675b2aabfb8d5829bb8df0a6e986b037
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html Modified 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-smarter-dutp.cwl

Branch/Commit ID: master
workflow graph workflow_input_format_expr.cwl

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

Path: testdata/workflow_input_format_expr.cwl

Branch/Commit ID: main
workflow graph EMG pipeline v3.0 (single end version)

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: master
workflow graph gaps_or_not.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: gaps_or_not.cwl

Branch/Commit ID: master
workflow graph createindex.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/createindex.cwl

Branch/Commit ID: master
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c
workflow graph map medium and long reads (> 100 bp) against reference genome

https://github.com/common-workflow-library/bio-cwl-tools.git

Path: bwa/BWA-Mem2-single.cwl

Branch/Commit ID: release
workflow graph msi.cwl

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/subworkflows/msi.cwl

Branch/Commit ID: master
workflow graph CWL-RNAseq.cwl

https://github.com/junyussh/RunningWorkflows-on-the-GoogleCloud.git

Path: CWL-RNAseq/CWL-RNAseq.cwl

Branch/Commit ID: master