Explore Workflows

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

Graph Name Retrieved From View
workflow graph Sort and merge input bed file and generate a .sorted.merged.bed file

https://github.com/swamyuma/cwl-tools.git

Path: sort_merge.cwl

Branch/Commit ID: 14be112d65ebb76f0368747099b5778f35d0387f
workflow graph waltz_workflow_all_bams.cwl

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

Path: workflows/waltz/waltz_workflow_all_bams.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3
workflow graph waltz-workflow.cwl

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

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3
workflow graph allele-process-strain.cwl

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 6e09b4bf1ff0eb3dd1294f5578624c5a2a2b0b37
workflow graph qc_workflow_wo_waltz.cwl

This workflow is intended to be used to test the QC module, without having to run the long waltz step

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

Path: workflows/QC/qc_workflow_wo_waltz.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3
workflow graph allele-process-reference.cwl

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

Path: subworkflows/allele-process-reference.cwl

Branch/Commit ID: 6e09b4bf1ff0eb3dd1294f5578624c5a2a2b0b37
workflow graph count-lines1-wf.cwl

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

Path: tests/count-lines1-wf.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37
workflow graph rnaseq-pe-dutp-mitochondrial.cwl

RNA-Seq strand specific mitochondrial workflow for pair-end experiment based on BioWardrobe's basic analysis.

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

Path: workflows/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: cf107bc24a37883ef01b959fd89c19456aaecc02
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: 8bf36bfad5624fbc8fc315e82783a44e9e5e4470
workflow graph protein_extract

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

Path: progs/protein_extract.cwl

Branch/Commit ID: c00944bae1a9d0f726f271786dae5454aa36f6e1