8000 Liftover to Graphmap2 nf-core module · Issue #302 · nf-core/nanoseq · GitHub
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mlgosh opened this issue Mar 24, 2025 · 1 comment
Open

Liftover to Graphmap2 nf-core module #302

mlgosh opened this issue Mar 24, 2025 · 1 comment
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@Graeme-Smith
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enhancement New feature or request

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@mlgosh
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mlgosh commented Mar 24, 2025

Description of feature

Nanoseq currently using a local Graphmap2 module, there is now a module available through nf-core
@mlgosh mlgosh added the enhancement New feature or request label Mar 24, 2025
@Graeme-Smith Graeme-Smith self-assigned this Mar 24, 2025
@Graeme-Smith
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Graeme-Smith commented Mar 24, 2025 •
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  • 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

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@Graeme-Smith Graeme-Smith

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enhancement New feature or request
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