Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 5e92165ac2c11608ab2db42fe2d66eabe72dbb40
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_qc.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
workflow graph Metagenomics workflow

Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon

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

Path: cwl/workflows/workflow_pilon_mapping.cwl

Branch/Commit ID: cd0c19d51068c5407cd70b718a561d4662819d87
workflow graph Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass2.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8