Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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readme-assembly-workflow.cwl
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https://github.com/nal-i5k/organism_onboarding.git
Path: flow_create_readme/readme-assembly-workflow.cwl Branch/Commit ID: master |
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PGAP Pipeline, simple user input, PGAPX-134
PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template) |
https://github.com/ncbi/pgap.git
Path: pgap.cwl Branch/Commit ID: master |
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Add snv and indel bam-readcount files to a vcf
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https://github.com/fgomez02/analysis-workflows.git
Path: definitions/subworkflows/vcf_readcount_annotator.cwl Branch/Commit ID: No_filters_detect_variants |
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Report generation workflow
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https://github.com/arvados/arvados-tutorial.git
Path: WGS-processing/cwl/helper/report-wf.cwl Branch/Commit ID: main |
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wf_self_consistency_ratio.cwl
Computes the self-consistency ratio (see Gabe's protocols paper, or CHIP SEQ). Given two replicates, split each and perform IDR on each fragment. Returns the ratio of max(N1, N2)/min(N1, N2) where N1, N2 are the numbers of reproducible peaks found between each rep split pair. |
https://github.com/YeoLab/merge_peaks.git
Path: cwl/wf_self_consistency_ratio.cwl Branch/Commit ID: master |
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cnv_gridss
CNV GRIDSS calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/cnv_gridss.cwl Branch/Commit ID: master |
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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: master |
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createindex_singlevirus.cwl
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https://github.com/yyoshiaki/virtus.git
Path: workflow/createindex_singlevirus.cwl Branch/Commit ID: master |
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chksum_seqval_wf_paired_fq.cwl
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https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_seqval_wf_paired_fq.cwl Branch/Commit ID: 0.4.0 |
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bqsr_workflow.cwl
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https://github.com/mskcc/Innovation-Pipeline.git
Path: workflows/BQSR/bqsr_workflow.cwl Branch/Commit ID: master |
