Explore Workflows

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

Path: flow_dispatch/2blat/workflow.cwl

Branch/Commit ID: 8b8c6dd16e06b43fbb50f1c0821856a31f1bbbc5

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c

**Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning**<br> - Workflow Nanopore Quality - Kraken2 taxonomic classification of FASTQ reads - Flye (de-novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) **When Illumina reads are provided:** - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - Assembly polishing with Pilon<br> - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2 - CheckM - BUSCO - GTDB-Tk **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> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br>

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

Path: cwl/workflows/workflow_nanopore_assembly.cwl

Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c

Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

https://github.com/datirium/workflows.git

Path: workflows/homer-motif-analysis-peak.cwl

Branch/Commit ID: 60854b5d299df91e135e05d02f4be61f6a310fbc

Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl

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

Path: structuralvariants/cwl/subworkflows/bwa_index.cwl

Branch/Commit ID: a4a3547b9790e99a58424a0dfcb4e467a7691d6a

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc

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

Path: structuralvariants/cwl/subworkflows/bwa_mem.cwl

Branch/Commit ID: 32a040f94e9798bf91858da51598f0d68c35797d

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

Path: vecscreen/foreign_screening.cwl

Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3