Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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RNA-seq alelle specific pipeline for paired-end data
Allele specific RNA-Seq paired-end workflow |
https://github.com/datirium/workflows.git
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 |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
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> |
https://git.wur.nl/unlock/cwl.git
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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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: workflows/emg-pipeline-v4-paired.cwl Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f |
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rnaseq-star-rsem-deseq2.cwl
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https://github.com/pitagora-network/DAT2-cwl.git
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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https://github.com/common-workflow-language/cwltool.git
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> |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_metagenomics_binning.cwl Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0 |
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split_bam_subpipeline.cwl
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https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git
Path: janis_pipelines/wgs_somatic/cwl/tools/split_bam_subpipeline.cwl Branch/Commit ID: ccca639fe0b3a8104ff9fcfa285f1134706032b8 |
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Feature expression merge - combines feature expression from several experiments
Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names. |
https://github.com/datirium/workflows.git
Path: workflows/feature-merge.cwl Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3 |
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exome_metrics.cwl
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https://github.com/nci-gdc/gdc-dnaseq-cwl.git
Path: workflows/bamfastq_align/exome_metrics.cwl Branch/Commit ID: dd7f86b3cc10eb1cda07dc2fc279ba2529c8ad61 |
