Explore Workflows

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Graph Name Retrieved From View
workflow graph preprocess fasta

Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/preprocess-fasta.workflow.cwl

Branch/Commit ID: 210a46717d091c186235d211c1175f02d0a644b6
workflow graph 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: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fastq.workflow.cwl

Branch/Commit ID: 210a46717d091c186235d211c1175f02d0a644b6
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fasta.workflow.cwl

Branch/Commit ID: 210a46717d091c186235d211c1175f02d0a644b6
workflow graph exomeseq.cwl#exomeseq-01-preprocessing.cwl

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

Path: packed/exomeseq.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: exomeseq-01-preprocessing.cwl
workflow graph Whole Exome Sequencing

Whole Exome Sequence analysis using GATK best practices - Germline SNP & Indel Discovery

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

Path: packed/exomeseq.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: main
workflow graph exomeseq.cwl#exomeseq-03-organizedirectories.cwl

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

Path: packed/exomeseq.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: exomeseq-03-organizedirectories.cwl
workflow graph exomeseq.cwl#exomeseq-02-variantdiscovery.cwl

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

Path: packed/exomeseq.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: exomeseq-02-variantdiscovery.cwl
workflow graph exomeseq.cwl#exomeseq-00-prepare-reference-data.cwl

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

Path: packed/exomeseq.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: exomeseq-00-prepare-reference-data.cwl