Explore Workflows

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

Graph Name Retrieved From View
workflow graph bacterial_orthology

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

Path: bacterial_orthology/wf_bacterial_orthology.cwl

Branch/Commit ID: 7cee09fb3e33c851e4e1dfc965c558b82290a785
workflow graph count-lines11-extra-step-wf.cwl

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

Path: tests/count-lines11-extra-step-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph timelimit4-wf.cwl

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

Path: tests/timelimit4-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph waltz-workflow.cwl

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

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: 7061957d31023d922501fba61310b2d82de61c15
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph protein_extract

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

Path: progs/protein_extract.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph qc_workflow.cwl

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

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: daba08457dd53fb81d11acb274c29a77b6122316
workflow graph draft_variation.cwl

https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git

Path: Variation/draft_variation.cwl

Branch/Commit ID: d5ad1d7fecdf3e1970429517fbdc21a8eae23ba5
workflow graph module-2.cwl

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

Path: workflows/module-2.cwl

Branch/Commit ID: e7754fb4d3cd14068eef0c498cc5c6fcf53dc31f
workflow graph RNA-Seq pipeline paired-end strand specific

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe-dutp.cwl

Branch/Commit ID: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb