Explore Workflows

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

Graph Name Retrieved From View
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph bam_filtering

BAM filtering

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c
workflow graph final-workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: final-workflow.cwl

Branch/Commit ID: b1e1b906fcfb2c0fad8811fb8ab03009282c1d19
workflow graph hisat2-stringtie_wf_pe.cwl

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.cwl

Branch/Commit ID: cd79f2db4b166d205456ab718e2581d6ab6e9f23
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_nonhuman.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph cnv_codex

CNV CODEX calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_codex.cwl

Branch/Commit ID: 26ae4914651d5b3e188028d1e9d88a391b3f6730
workflow graph genomics-workspace-genome.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl

Branch/Commit ID: aa375dcaa5ccfbb4e2aa4433d10948c641b044eb
workflow graph Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass1.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph genomics-workspace-protein.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-protein.cwl

Branch/Commit ID: aa375dcaa5ccfbb4e2aa4433d10948c641b044eb
workflow graph Read quality control, trimming and contamination filter.

Workflow for (paired) read quality control, trimming and contamination filtering. Will output a merged set of read pairs, when multiple datasets are used. Steps: - FastQC (read quality control) - fastp (read quality trimming) - Kraken2 taxonomic classification of reads - bbduk used for phix and/or rrna filtering - bbmap for (contamination) filtering

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

Path: cwl/workflows/workflow_illumina_quality.cwl

Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae