Explore Workflows

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

Graph Name Retrieved From View
workflow graph bwa_mem

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

Path: structuralvariants/subworkflows/bwa_mem.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f
workflow graph cnv_gridss

CNV GRIDSS calling

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

Path: structuralvariants/subworkflows/cnv_gridss.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f
workflow graph picard_markduplicates

Mark duplicates

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

Path: structuralvariants/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f
workflow graph bwa_index

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

Path: structuralvariants/subworkflows/bwa_index.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f
workflow graph SSU-from-tablehits.cwl

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 9c57dba558a4e04a1884eae1df8431dcaccafc1e
workflow graph tt_univec_wnode.cwl

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: 1e7aa9f0c34987ddafa35f9b1d2c77d99fafbdab
workflow graph FASTQ Vector Removal

This workflow clean up vectros from fastq files

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Contamination/fastq-vector-removal.cwl

Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419
workflow graph Illumina read quality control, trimming and contamination filter.

**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple read pairs will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - Kraken2 for taxonomic classification of reads<br /> - BBduk for phix and rRNA filtering<br /> - BBmap for (contamination) filtering using given references<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.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_illumina_quality.cwl

Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3
workflow graph Non-Coding Bacterial Genes

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

Path: bacterial_noncoding/wf_bacterial_noncoding.cwl

Branch/Commit ID: 5cc4af517f82f4cda3023644d61abd85cbc1fc18