Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
workflow graph sec-wf-out.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c
workflow graph 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
workflow graph func_ann_and_post_processing-subwf.cwl

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/assembly/func_ann_and_post_processing-subwf.cwl

Branch/Commit ID: fff6fa392370b56e1fe7c374167ba73df3018775
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: cc7fb3e5c534036638921878527a610fd5e1c2ab
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph Indices builder from GBOL RDF (TTL)

Workflow to build different indices for different tools from a genome and transcriptome. This workflow expects an (annotated) genome in GBOL ttl format. Steps: - SAPP: rdf2gtf (genome fasta) - SAPP: rdf2fasta (transcripts fasta) - STAR index (Optional for Eukaryotic origin) - bowtie2 index - kallisto index

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_indexbuilder.cwl

Branch/Commit ID: master
workflow graph echo-wf-default.cwl

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

Path: tests/echo-wf-default.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050
workflow graph workflow_mock_ngtax.cwl

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_mock_ngtax.cwl

Branch/Commit ID: master