Version 1.3.0 pre-release

[tkchafin]

[1.3.0] - Antipodean Opaleye - [2024-08-20]

Enhancements & fixes

• Combined steps to improve the efficiency of the pipeline, especially on large genomes
• "crumble" is now run on every data type, not just PacBio
• Added options for output format and to turn on/off crumble compression (Give user control of output format and compression  #107)
• Added fastq as possible input type for PacBio (Pacbio fastq #106) and Illumina/HiC (add input type fastq.gz and fq.gz for Illumina and HiC reads #96)
• Disabled running bwa index when no short-read data provided (Disable BWAMEM2 index when no short reads data #100)
• Added support for optional custom SAM header (Option to incorporate additional metadata from provided SAM header file #95)
• Switch to nf-validation (nf-core v2.14 update #99) and further updates for nf-core v2.14 compliance (Template update for nf-core/tools version 2.14.1 #98)

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
blastn	2.13	2.15
minimap2	2.24	2.28
samtools	1.14 and 1.17	1.20
seqkit		2.8.1
seqtk		1.4

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

Parameters

Old parameter	New parameter
	'--header'
	'--outfmt'
	'--compression

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

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
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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).

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @tkchafin,

It looks like this pull-request is has been made against the tkchafin/readmapping main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the tkchafin/readmapping dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[muffato]

Just pushed a commit to fix a few nf-core/readmapping. Otherwise good to go 👍🏼