Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 6b365b79675b2aabfb8d5829bb8df0a6e986b037
workflow graph qiime2 rarefaction visualization

Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/duke-gcb/bespin-cwl.git

Path: packed/qiime2-step3-alpha-analysis.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: qiime2-07-alpha-rarefaction.cwl
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
workflow graph readgroup_fastq_pe.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroup_fastq_pe.cwl

Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f
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: 174f3b239018328cec1d821947438b457552724c