Explore Workflows

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

Graph Name Retrieved From View
workflow graph project-workflow-sv.cwl

https://github.com/mskcc/argos-cwl.git

Path: project-workflow-sv.cwl

Branch/Commit ID: 9afe0b169cff4df57d5a5cbf18c6e34d5cdc6998
workflow graph mini-ST610106.cwl

https://github.com/Marco-Salvi/dtc61.git

Path: mini-ST610106.cwl

Branch/Commit ID: 668634ce0f044d6e9ccdbd839b015d384cbfb0ab
workflow graph Prepare user input

Prepare user input for NCBI-PGAP pipeline

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

Path: prepare_user_input2.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph secret_wf.cwl

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40
workflow graph search.cwl#main

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

Path: tests/search.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3

Packed ID: main
workflow graph ChIPseq_pipeline_spike_in.cwl

https://github.com/CompEpigen/ChIPseq_workflows.git

Path: CWL/workflows/ChIPseq_pipeline_spike_in.cwl

Branch/Commit ID: b7709bff6bd6e93a28dfc2fee0655f6aceef0901
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: f401b02285f30de1c12ac2859134099fe04be33f
workflow graph Deprecated. Single-cell Assign Cell Types

Deprecated. Single-cell Assign Cell Types ========================================= Assigns cell types to Seurat clusters.

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

Path: workflows/sc-assign-cell-types.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
workflow graph RNA-Seq pipeline single-read

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-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9