Explore Workflows

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

Graph Name Retrieved From View
workflow graph final-workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: final-workflow.cwl

Branch/Commit ID: master
workflow graph Trim Galore RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-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 file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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 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/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d
workflow graph scatter-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl

Branch/Commit ID: 5ef2516220cd2ed327ba7966e7d812de969f4eea

Packed ID: main
workflow graph cond-wf-010_nojs.cwl

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

Path: tests/conditionals/cond-wf-010_nojs.cwl

Branch/Commit ID: main
workflow graph epigenome-chip-seq.packed.cwl#main

https://github.com/pitagora-network/DAT2-cwl.git

Path: workflow/epigenome-chip-seq/epigenome-chip-seq.packed.cwl

Branch/Commit ID: main

Packed ID: main
workflow graph wffail.cwl

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: main
workflow graph STAR-RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq_star_fusion.cwl

Branch/Commit ID: master
workflow graph varscan somatic workflow

https://github.com/genome/cancer-genomics-workflow.git

Path: varscan/varscan.cwl

Branch/Commit ID: toil_compatibility
workflow graph GSC Paired Jobs

Serial combination of KnowEnG tools

 https://github.com/KnowEnG-Research/cwl-specification.git

Path: code/workflow.gsc.cwl

Branch/Commit ID: master
workflow graph touch_ls_wf.cwl

https://github.com/jeremiahsavage/toy-cwl.git

Path: touch_ls_wf.cwl

Branch/Commit ID: master