Explore Workflows

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Graph Name Retrieved From View
workflow graph RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

 https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/rna-selector.cwl

Branch/Commit ID: f993cada89d2c6f7480a0d56baa7836a361b1f3a
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-dutp-mitochondrial.cwl

Branch/Commit ID: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
workflow graph EMG pipeline v3.0 (single end version)

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph rnaseq-alignment-quantification

This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator

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

Path: workflows/RNA-Seq/rnaseq-quantification-qc.cwl

Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419
workflow graph EMG pipeline v4.0 (single end version)

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v4-single.cwl

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph Single-cell Reference Indices

Single-cell Reference Indices ============================================================= Builds a Cell Ranger and Cell Ranger ARC compatible reference folders from the custom genome FASTA and gene GTF annotation files

 https://github.com/Barski-lab/scRNA-Seq-Analysis.git

Path: workflows/sc-ref-indices-wf.cwl

Branch/Commit ID: 280cad66c2a5b2e1b66e4f8a5469942e88df5b74
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: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c
workflow graph EMG pipeline v3.0 (single end version)

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: fa86fce570ab91c624272c8ffda672069d2f276d
workflow graph kallisto_scatter_synapse_single_end_workflow.cwl

https://github.com/CRI-iAtlas/iatlas-workflows.git

Path: Kallisto/workflow/kallisto_scatter_synapse_single_end_workflow.cwl

Branch/Commit ID: 3acab4d22ff0f9657dc8c5685799898a2fc2fd25
workflow graph EMG pipeline v3.0 (paired end version)

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3-paired.cwl

Branch/Commit ID: 25129f55226dee595ef941edc24d3c44414e0523