Explore Workflows

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

Graph Name Retrieved From View
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f
workflow graph io-file-default-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/io-file-default-wf.cwl

Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df
workflow graph scatter-wf3.cwl#main

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-wf3.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37

Packed ID: main
workflow graph module-2.cwl

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

Path: workflows/module-2.cwl

Branch/Commit ID: 0bd60a8962cc9960b7e4f6528547e220bcd2b941
workflow graph Feature expression merge - combines feature expression from several experiments

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

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

Path: workflows/feature-merge.cwl

Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620
workflow graph module-1.cwl

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

Path: workflows/module-1.cwl

Branch/Commit ID: 0bd60a8962cc9960b7e4f6528547e220bcd2b941
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: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9
workflow graph count-lines1-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534
workflow graph sbg_cwl_test.cwl

https://github.com/li-xinshan/data_visualization.git

Path: sbg_cwl/sbg_cwl_test.cwl

Branch/Commit ID: dev
workflow graph cnv_exomedepth

CNV ExomeDepth calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: 572d9e6b9264d98967b33d18110b0e1979b21d6c