Liftover to Graphmap2 nf-core module

[mlgosh]

Description of feature

Nanoseq currently using a local Graphmap2 module, there is now a module available through nf-core

[Graeme-Smith]

• Add Modules to Pipelines

Two modules in nf-core:
graphmap2/align │
graphmap2/index

• Install module to the pipeline

• Add include statement at the top of the pipeline’s (sub)workflow to import module (as suggested by nf-core modules install)

• Insert module execution into the relevant place (sub)workflow script TOOL(ch_input)

• Make sure to mix in the module’s version into the version channel, e.g. ch_versions = ch_versions.mix(TOOL.out.versions)

• Make sure to mix any output files for MultiQC into a relevant channel, e.g. ch_multiqc_files = ch_multiqc.mix(TOOL.out.log)

• Create a section in conf/modules.conf for the module (with a default results directory and output file pattern)

• Add any necessary parameters for the module with defaults to nextflow.config

• Insert any pipeline level parameters (params.*) into the ext.args of corresponding conf/modules.config

• Add a citation for the new tool/module to citations.md

• Update docs/USAGE.md to describe any important information about running of the module (this can be optional in some cases)

• Update docs/OUTPUT.md to describe the directories output files of the module

• Update README.md mentioning the tool is used and any pipeline diagrams (optional)

• If not already installed, install prettier (prettier can also be installed using Conda) and then run it formatting on the whole repository

• Run a local test of the pipeline with the included new functionality to check it works.

• Delete local Graphmap2 files