Explore Workflows

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

Graph Name Retrieved From View
workflow graph Generate ATDP heatmap using Homer

Generate ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

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

Path: workflows/heatmap.cwl

Branch/Commit ID: ddc35c559d1ac6aab4972fe1a2b63300c4373f54
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: e4d6182d5f7a6a880e5f2b21273cf40d25e187df
workflow graph count-lines15-wf.cwl

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

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: a70a83fe14a100cd16e2402ec17b2904f5eeb17d
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

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-dutp.cwl

Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b
workflow graph wf.cwl

https://github.com/ResearchObject/runcrate.git

Path: tests/data/no-output-run-1/snapshot/wf.cwl

Branch/Commit ID: 802bd3c43696c88821f75c3ec528573e06679521
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: b548dc1ec6cb90d14d57a813fb69430adaa1c425
workflow graph CreateSymlink-workflow.cwl

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

Path: CreateSymlink-workflow.cwl

Branch/Commit ID: 096a9feffe292a1aeb329552661d27bb579e084c