Explore Workflows

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

Graph Name Retrieved From View
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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 file 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/rnaseq-se-dutp-mitochondrial.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph scRNA-seq pipeline using Salmon and Alevin

https://github.com/hubmapconsortium/visium-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: 37af2055e751f8c8ca68757648f24ea290bf5291
workflow graph scatter-wf3.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl

Branch/Commit ID: f997d13af87216e9b5048c732a511053c7ba714c

Packed ID: main
workflow graph steplevel-resreq.cwl

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

Path: cwltool/schemas/v1.0/v1.0/steplevel-resreq.cwl

Branch/Commit ID: f207d168f4e7eb4dd2279840d4062ba75d9c79c3
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73
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