Explore Workflows
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RNA-Seq pipeline paired-end strand specific
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 |
![]() Path: workflows/rnaseq-pe-dutp.cwl Branch/Commit ID: d6ec0dee61ef65a110e10141bde1a79332a64ab0 |
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Illumina read quality control, trimming and contamination filter.
**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple paired datasets will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - BBduk for phiX and (optional) rRNA filtering<br /> - Kraken2 for taxonomic classification of reads (optional)<br /> - BBmap for (contamination) filtering using given references (optional)<br /> - FastQC on filtered (merged) data<br /> **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default |
![]() Path: cwl/workflows/workflow_illumina_quality.cwl Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0 |
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811.cwl
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![]() Path: tests/wf/811.cwl Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429 |
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RNA-seq alelle specific pipeline for paired-end data
Allele specific RNA-Seq paired-end workflow |
![]() Path: workflows/allele-rnaseq-pe.cwl Branch/Commit ID: d6ec0dee61ef65a110e10141bde1a79332a64ab0 |
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FASTQ Vector Removal
This workflow clean up vectros from fastq files |
![]() Path: workflows/File-formats/remove-fastq-reads-from-blast.cwl Branch/Commit ID: b8f18a03ffbd7d5b78a7f220686b81d539686e98 |
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Metagenomic Binning from Assembly
Workflow for Metagenomics from raw reads to annotated bins.<br> Summary - MetaBAT2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification) - BUSCO (bin completeness) **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br> |
![]() Path: cwl/workflows/workflow_metagenomics_binning.cwl Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0 |
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EMG pipeline v4.0 (paired end version)
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![]() Path: workflows/emg-pipeline-v4-paired.cwl Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f |
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rnaseq-star-rsem-deseq2.cwl
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![]() Path: workflow/rna-seq/rnaseq-star-rsem-deseq2/rnaseq-star-rsem-deseq2.cwl Branch/Commit ID: 6db4456ca7314b036e59f50910654066da99772a |
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scatterfail.cwl
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![]() Path: tests/wf/scatterfail.cwl Branch/Commit ID: 2710cfe731374cf7244116dd7186fc2b6e4af344 |
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Metagenomic Binning from Assembly
Workflow for Metagenomics from raw reads to annotated bins.<br> Summary - MetaBAT2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification) - BUSCO (bin completeness) **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br> |
![]() Path: cwl/workflows/workflow_metagenomics_binning.cwl Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0 |