Prepare 2.3.0

[charles-plessy]

Preparation of the 2.3.0 release.

Provisional changelog: Points in bold belong to this pull request. After the PR is accepted I will directly push to dev a small commit changing the version number from 2.3.0dev to 2.3.0 in order to prepare the release PR to the master branch, or please tell me if the standard procedure is different.

Regarding #103 , the SVG source of the tubemap PNG looking bad on GitHub and mabye on Mac/Windows as well, I still do not know how to solve it, but on my Linux box the Inkscape view is like what you can see on the PNG.

v2.3.0 "Umi budou" - [TBD]

Added

• New --multi_cram option to produce a multi-query CRAM file combining all the alignments (#60).
• New --multiqc_thumbs option to produce alignment thumbnails in the MultiQC report (#93).
• New --strand option to index only one strand of the genome, which reduces memory usage at the expense of speed, and suppresses -/+ alignments (#97).
• New --query and --queryName convenience options to skip samplesheet creation when there is only one query genome to align (#112).
• In the GFF export format, the target genome sequence lenghts are now exported in ##sequence-region fields (#70).

Fixed

• Using the nf-core version of the FASTA_BGZIP_INDEX_DICT_SAMTOOLS subworkflow that we just contributed.
• Check for input file existence in the parameter schema #73).

Parameters

Old parameter	New parameter
	--multi_cram
	--multiqc_thumbs
	--query
	--queryName
	--strand

Dependencies

Dependency	Old version	New version
SAMTOOLS_BGZIP	1.21
SAMTOOLS_DICT	1.21	1.23.1
SAMTOOLS_FAIDX	1.21	1.23.1
SAMTOOLS_MERGE		1.23.1
HTSLIB_BGZIPTABIX		1.23.1

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/pairgenomealign branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).