Explore Workflows

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

Graph Name Retrieved From View
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: c6e7e18969c761803c38762ad6ee91b0001c52e2
workflow graph rnaseq-pe-dutp.cwl

RNA-Seq basic analysis workflow for strand specific paired-end experiment.

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

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph scatter-valuefrom-wf5.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-valuefrom-wf5.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4
workflow graph tt_kmer_compare_wnode

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 9e43bc5cff985574e1f8135d4c50b5a347517c9e
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 86fbeb95ef85111f3b4c6bc2bba8f06cef64e157
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: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/wgs_alignment.cwl

Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00
workflow graph QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data

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

Path: workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph step-valuefrom3-wf_v1_2.cwl

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

Path: testdata/step-valuefrom3-wf_v1_2.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/Barski-lab/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d