Explore Workflows

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

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

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

Path: v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e
workflow graph abra_workflow.cwl

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

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: f874bd8a9bb7da9839f0aa6be708d5d16f72945d
workflow graph iwdr_with_nested_dirs.cwl

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389
workflow graph allele-process-strain.cwl

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 2d00e7f29c72d33b70dcd46b58db1fc31a7f2d86
workflow graph conflict.cwl#main

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

Path: tests/wf/conflict.cwl

Branch/Commit ID: 4642316a30a95d4f3d135c18f98477886b160094

Packed ID: main
workflow graph unifiedgenotyper.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/unifiedgenotyper.cwl

Branch/Commit ID: 13c106834d6c9031de08496faeff521740a0c95f
workflow graph search.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389

Packed ID: main
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 686b570a9fa46f3ace3f8e9935490b75df86a1fc
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: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d