Explore Workflows

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

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

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

Path: project-workflow.cwl

Branch/Commit ID: 82a391eb588505a87e2f549b662fa68214076dd4
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_molecular.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d
workflow graph secret_wf.cwl

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375
workflow graph Compute library complexity

This workflow compute library complexity

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/bedtools-bam-pbc.cwl

Branch/Commit ID: ebf1dd3c243c08634b0b3d9766c0a354903920ee
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fastq.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a
workflow graph Single-Cell ATAC-Seq Filtering Analysis

Single-Cell ATAC-Seq Filtering Analysis Removes low-quality cells from the outputs of either the “Cell Ranger Count (ATAC)” or “Cell Ranger Aggregate (ATAC)” pipeline. The results of this workflow are used in the “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipeline.

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

Path: workflows/sc-atac-filter.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph step-valuefrom2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph RNA-Seq pipeline paired-end

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.cwl

Branch/Commit ID: c602e3cdd72ff904dd54d46ba2b5146eb1c57022