Explore Workflows
View already parsed workflows here or click here to add your own
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merge and annotate svs with population allele freq and vep
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: c235dc6d623879a6c4f5fb307f545c9806eb2d23 |
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Metagenomics workflow
Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - Contig binning (OPTIONAL) |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_metagenomics_assembly.cwl Branch/Commit ID: master |
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Spliced RNAseq workflow
Workflow for Spliced RNAseq data Steps: - workflow_illumina_quality: - FastQC (Read Quality Control) - fastp (Read Trimming) - STAR (Read mapping) - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts) |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_RNAseq_Spliced.cwl Branch/Commit ID: master |
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tt_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: f3bc91cf1320f75967ec2719b1506b75f23cb4b6 |
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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 |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_illumina_quality.cwl Branch/Commit ID: master |
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gcaccess_from_list
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https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3 |
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iwdr-passthrough-successive.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/iwdr-passthrough-successive.cwl Branch/Commit ID: 1397d96ad97fe8abfd1184675d728a8a04699d67 |
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bam to trimmed fastqs and HISAT alignments
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2 |
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sec-wf-out.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/sec-wf-out.cwl Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c |
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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: master |
