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[RELEASE PR for 2.3.0 release] #305

Merged
merged 258 commits into from
Feb 23, 2024
Merged

[RELEASE PR for 2.3.0 release] #305

merged 258 commits into from
Feb 23, 2024

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apeltzer
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@apeltzer apeltzer commented Jan 24, 2024

PR checklist

Full Changelog:

v2.3.0 - 2024-02-23 - Gray Zinc Dalmatian

  • [#307] - Clean up config file and improve output folder structure
  • [#299] - Bugfix for missing inputs in BAM stats (genome_quant.r)
  • [#164] - UMI Handling Feature implemented in the pipeline
  • [#302] - Merged in nf-core template v2.11.1
  • [#294] - Fixed contamination screening issues
  • [#309] - Merged in nf-core template v2.12.0
  • [#310] - Removed unnecessarily separate mirtrace subworkflow, now using module instead
  • [#311] - Fix use of FASTP, set three_prime_adapter per default
  • [#314] - Add parameters to control publishing of intermediate results
  • [#317] - Fixed issue with bowtie indices directly supplied
  • [#318] - Merged in nf-core template v2.13.0 and pinned nf-validator

Parameters

Old parameter New parameter
--with_umi
--umitools_extract_method
--umitools_method
--skip_umi_extract
--umitools_bc_pattern
--umi_discard_read
--save_umi_intermeds
--save_aligned
--save_aligned_mirna_quant
--save_merged

Software dependencies

Dependency Old version New version
multiqc 1.15 1.20
edgeR 3.36.0 4.0.2
limma 3.50.0 3.58.1
bioconvert 0.4.3 1.1.1
mirdeep 2.0.1 2.0.1.3
seqkit 2.3.1 2.6.1
fastqc 0.11.4 0.12.1
samtools 1.17 1.19.2
umitools 1.1.5
umicollapse 1.0.0
  • 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/smrnaseq branch on the nf-core/test-datasets repository.
  • 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).

CKComputomics and others added 30 commits June 15, 2022 13:55
Added additional configuration to change the output file name of
samtools sort.
Added the documentation detailing the output files of the UMI-tools
deduplication step.
After deduplication the reads that remained unaligned to the
provided reference genome are merged with the set of deduplicated
reads to enable the use of the full spectrum of reads, independent
of potential reference bias. This behaviour can be deactivated by
setting --umi_merge_unmapped false
Information on the new --umi_merge_unmapped command were added to
both the CHANGELOG, as well as the output markdown script.
Includes the nf-core cat module to replace the custom concatenation
module.
Implements the use of the nf-core cat module.
deletes the now unused conatenation module.
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@christopher-mohr christopher-mohr left a comment

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Done with first 100 files, will continue later.

CHANGELOG.md Outdated Show resolved Hide resolved
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@nvnieuwk nvnieuwk left a comment

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LGTM :), although I've not had a look at everything so please don't take my review as a full review

Co-authored-by: Christopher Mohr <[email protected]>
@apeltzer
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Will also wait for @christopher-mohr 's final words. And running a few combination tests locally on our HPC to be safe. These few hours are not going to hurt anymore ;-)

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LGTM

@apeltzer apeltzer merged commit c611b15 into master Feb 23, 2024
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9 participants