Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines3-wf.cwl

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

Path: tests/count-lines3-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph analysis for assembled sequences

rna / protein - qc, annotation, index, abundance

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

Path: CWL/Workflows/assembled.workflow.cwl

Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4
workflow graph steplevel-resreq.cwl

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

Path: cwltool/schemas/v1.0/v1.0/steplevel-resreq.cwl

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 4a44218a713aecc488359be275409414ae8c1434
workflow graph bam to trimmed fastqs

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-dutp.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph scatter-valuefrom-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: 55ccde7c2fe3e7899136ce8606a341e292d7050a
workflow graph Single-cell RNA-Seq Filtering Analysis

Single-cell RNA-Seq Filtering Analysis Filters single-cell RNA-Seq datasets based on the common QC metrics.

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

Path: workflows/sc-rna-filter.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e