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: ad948b2691ef7f0f34de38f0102c3cd6f5182b29
workflow graph js-expr-req-wf.cwl#wf

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb

Packed ID: wf
workflow graph exomeseq-03-organizedirectories.cwl

https://github.com/duke-gcb/bespin-cwl.git

Path: subworkflows/exomeseq-03-organizedirectories.cwl

Branch/Commit ID: e82f3a71183048dd6700ec6725ee526ac1a95238
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 8d8512061f2367c90aac67bcbf92af1061b4af59
workflow graph filter-pcr-artifacts.cwl

DNase-seq - map - Filter PCR Artifacts

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/map/filter-pcr-artifacts.cwl

Branch/Commit ID: 6da8cef69f3a585fc3e2f4f2f730d361cbe2e978
workflow graph count-lines13-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: cb81b22abc52838823da9945f04d06739ab32fda
workflow graph chipseq-header.cwl

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

Path: metadata/chipseq-header.cwl

Branch/Commit ID: 2f0db4b3c515f91c5cfda19c78cf90d339390986
workflow graph env-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl

Branch/Commit ID: cb81b22abc52838823da9945f04d06739ab32fda
workflow graph any-type-compat.cwl

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

Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl

Branch/Commit ID: fc6ca8b1498926f705dcfde7ab0a365bd09a9675
workflow graph functional analysis prediction with InterProScan

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/functional_analysis.cwl

Branch/Commit ID: 2104dc36c775de93de3fef77e7f82a19da76b6e3