Explore Workflows

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

Graph Name Retrieved From View
workflow graph sum-wf.cwl

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

Path: tests/sum-wf.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph ValidationWorkflowMissing

This is a placeholder for a missing acceptance workflow.

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

Path: workflows/ValidationWorkflowMissing.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
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: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726
workflow graph Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

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

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph wf-loadContents2.cwl

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

Path: tests/wf-loadContents2.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: 5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc
workflow graph cond-wf-009_nojs.cwl

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

Path: tests/conditionals/cond-wf-009_nojs.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph step-valuefrom2-wf_v1_2.cwl

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

Path: testdata/step-valuefrom2-wf_v1_2.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb