Available Subworkflows
Subworkflows combine modules into reusable groups of processes for Nextflow DSL2 pipelines. These subworkflows are maintained in the sanger-tol/nf-core-modules repository. For guidance on writing subworkflows, see the nf-core documentation.
6 subworkflows; Clear filters
Maps Hi-C reads in unaligned CRAM format to a set of references.
8 components; 4 pipelines
Scaffold a set of assemblies using YaHS and RagTag. YaHS is used to scaffold the first provided assembly, and then RagTag is used to scaffold the remaining assemblies using the first scaffolded assembly as a reference. Finally the RagTag scaffolds are re-scaffolded using YaHS to correct errors.
5 components; 0 pipelines
Scaffold an assembly FASTA file using Hi-C contacts with YaHS.
4 components; 1 pipelines
Build contact maps from pairs files using PretextMap, Juicertools, and Cooler
6 components; 2 pipelines
Regenerate a Pretext contact map after manual curation in PretextView. Corrects the curated AGP
onto the input assembly (pretext2asm), remaps Hi-C contacts with juicerc, builds a pairs file
(pretext/makepairs), and runs pretextmap.
4 components; 0 pipelines