Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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chipseq-gen-bigwig.cwl
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https://github.com/datirium/workflows.git
Path: subworkflows/chipseq-gen-bigwig.cwl Branch/Commit ID: 7a4593d2fa5b2fcbedc9219dc5687a4bc5aea66a |
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Trim Galore 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-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.cwl Branch/Commit ID: 799575ce58746813f066a665adeacdda252d8cab |
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EMG pipeline v3.0 (paired end version)
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https://github.com/proteinswebteam/ebi-metagenomics-cwl.git
Path: workflows/emg-pipeline-v3-paired.cwl Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193 |
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transform.cwl
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https://github.com/NCI-GDC/gdc-dnaseq-cwl.git
Path: workflows/dnaseq/transform.cwl Branch/Commit ID: dd7f86b3cc10eb1cda07dc2fc279ba2529c8ad61 |
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cmanalysis.cwl
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https://github.com/CERIT-SC/fireprot.git
Path: cmanalysis.cwl Branch/Commit ID: a2b0c18f117dcf2b0d7e33c59c0f180b6a9bf709 |
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Cut-n-Run pipeline paired-end
Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed |
https://github.com/datirium/workflows.git
Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: 2c486543c335bb99b245dfe7e2f033f535efb9cf |
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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: 9bf0aa495735f8081bb5870cb32fc898b9e6eb22 |
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FASTQ Vector Removal
This workflow clean up vectros from fastq files |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/File-formats/remove-fastq-reads-from-blast.cwl Branch/Commit ID: 6eb7fec3bd018addf02bb3285cb56d9453319d5d |
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broad-best-practice-data-pre-processing-workflow-4-1-0-0_decomposed.cwl
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https://github.com/svonworl/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow.git
Path: broad-best-practice-data-pre-processing-workflow-4-1-0-0_decomposed.cwl Branch/Commit ID: fe43d13c174816704f1d7941dc8cb5fce358c0de |
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Cut-n-Run pipeline paired-end
Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed |
https://github.com/datirium/workflows.git
Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: 8a92669a566589d80fde9d151054ffc220ed4ddd |
