new subworkflow: CONTACT_MAPS_INGEST_TRACKS

[DLBPointon]

CPretext imports currently looks like:

//LOCAL MODULES
include { PRETEXT_GRAPH as PRETEXT_INGEST_SNDRD             } from '../modules/local/pretext/graph/main'
include { PRETEXT_GRAPH as PRETEXT_INGEST_HIRES             } from '../modules/local/pretext/graph/main'
include { PRETEXT_GRAPH as PRETEXT_INGEST_ULTRA             } from '../modules/local/pretext/graph/main'

// LOCAL SUBWORKFLOWS
include { ACCESSORY_FILES                                   } from '../subworkflows/local/accessory_files/main'

// SANGER-TOL SUBWORKFLOWS
include { CRAM_MAP_ILLUMINA_HIC as ALIGN_CRAM               } from '../subworkflows/sanger-tol/cram_map_illumina_hic/main'
include { PAIRS_CREATE_CONTACT_MAPS as CREATE_MAPS_STDRD    } from '../subworkflows/sanger-tol/pairs_create_contact_maps/main'
include { PAIRS_CREATE_CONTACT_MAPS as CREATE_MAPS_HIRES    } from '../subworkflows/sanger-tol/pairs_create_contact_maps/main'
include { PAIRS_CREATE_CONTACT_MAPS as CREATE_MAPS_ULTRA    } from '../subworkflows/sanger-tol/pairs_create_contact_maps/main'

PRETEXT_GRAPH and PAIRS_CREATE_CONTACT_MAPS happen in pairs, to simplify we should just have a subworkflow which wraps the required logic.

Would mean making pretext/graph a more sensible module:
https://github.com/sanger-tol/curationpretext/tree/main/modules/local/pretext/graph

Could also complete
nf-core/modules#6494

Note

Jim's made me realise i should put how i intend to use the subworkflow

Import once and then modify the meta so that it gets run meta.resolution number of times (e.g. standard, hires, ultra). Would clean the whole thing up alot.

Is there an existing subworkflow for this?

• I have searched for the existing subworkflow

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Are you going to work on this?

• If I'm planning to work on this subworkflow, I added myself to the Assignees to facilitate tracking who is working on the subworkflow

[DLBPointon]

    withName: ".*:CREATE_MAPS:PRETEXTMAP" {
        cpus    = {  6       * task.attempt }
        memory  = {  ( meta.resolution == "standard" ? 3.GB : meta.resolution == "hires" ? 20.GB : meta.resolution == "ultra" ?: 40.GB )  * task.attempt }
        time    = {  1.h     * ( ( fasta.size() < 4e9 ? 24 : 48 ) * Math.ceil( task.attempt * 1 ) ) }
    }