Move to 2.2.0

[Thibault-Poinsignon]

Version 2.2.0

Added

• Subworkflows meta.yml
• Module FAIDX for chromosomes sizes calculation
• TRIMGALORE module for 5' clipping (see Improve pipeline for Arima Hi-C protocol #225)
• CALDER2 compartments calling (see '--compartments_caller' option)
• Local FILTER_CHROMSIZE module (in order to apply CALDER2 without error)
• Optional '--min_size' parameter for chromosome selection
• Default MIN_FRAG_SIZE, MAX_FRAG_SIZE, MIN_INSERT_SIZE and MAX_INSERT_SIZE values for Arima and ArimV2 protocols

Removed

• Module GETCHROMSIZES (replaced by FAIDX)
• Version channels from subworkflows (tools versions gathering still a WIP)

Fixed

• MATPLOTLIB warning derails parsing cooltools version in collated_versions.yml during NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS #227: MPLCONFIGDIR is set to "${baseDir}/mplconfig"
• reported bugs #62: a single number can be given as BIN_SIZES without error
• Improve pipeline for Arima Hi-C protocol #225:TRIMGALORE remove the first 5 bases of the 5' end and
  fragments and inserts size min/max settings are set to recommended values if Arima/ArimaV2 is used
• Bug from COOLER_CLOAD deprecated "pairs" ext.args calling
• Bug on the cooler "add resolution" step caused by module COOLER_CLOAD update

Updated

• All nf-core modules (including topics channel)
• Modules path
• "channel" syntax with lowercase c
• Components names in subworkflows meta.yml
• COOLER_CLOAD inputs and outputs
• BWA_MEM inputs
• SAMTOOL_SORT inputs
• UTILS_NFSCHEMA_PLUGIN inputs and outputs
• Markdown settings
• Template files
• nf-core version to 3.5.0

PR checklist

• This comment contains a description of changes (with reason).
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,singularity --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[maxulysse]

This version looks good to me ! thank you @Thibault-Poinsignon @maxulysse, any advice for the tests which are still failing ? Could we move forward like this. We would like to release a new stable version asap.

I'd recommend to try and merge #233 and/or #234 to have a minimal test using nf-test

[Thibault-Poinsignon]

All the checks are now successful with the two template updates. I'm running some full tests again to verify that everything is still working properly.

[ewels]

@nf-core-bot fix linting

[Thibault-Poinsignon]

It should be good to go

[nservant]

all good to me