Explore Workflows

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Graph Name Retrieved From View
workflow graph Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: e99e80a2c19682d59947bde04a892d7b6d90091c
workflow graph search.cwl#main

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

Path: tests/search.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de

Packed ID: main
workflow graph Trim Galore 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 **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.cwl

Branch/Commit ID: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d
workflow graph inp_update_wf.cwl

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

Path: tests/inp_update_wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph Bisulfite alignment and QC

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph Transcripts annotation workflow

https://github.com/EBI-Metagenomics/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-i5only-wf.cwl

Branch/Commit ID: 72f702591368397f56d455128f60916902104dd2
workflow graph gaps_or_not.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: gaps_or_not.cwl

Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f
workflow graph bulk scRNA-seq pipeline using Salmon

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: bulk-pipeline.cwl

Branch/Commit ID: a5779cc2804edf3052e597ea32f1f1c49aa33afb
workflow graph tt_kmer_compare_wnode

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca