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Merge pull request #1384 from nf-core/dev
Dev -> Master for 3.15.1
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‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16
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### Enhancements & fixes
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- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev
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- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names
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- [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules
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- [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing
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- [P$ #1383](https://github.com/nf-core/rnaseq/pull/1383) - Prerelease 3.15.1 version bumps
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## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04
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### Credits

‎modules.json

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‎modules/local/deseq2_qc/environment.yml

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name: deseq2_qc
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- conda-forge::r-base
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- conda-forge::r-optparse

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name: gtf2bed
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- conda-forge::perl=5.26.2

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name: gtf_filter
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- conda-forge::python=3.9.5

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name: multiqc_custom_biotype
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channels:
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dependencies:
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- conda-forge::python=3.9.5

‎modules/local/preprocess_transcripts_fasta_gencode/environment.yml

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name: preprocess_transcripts_fasta_gencode
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channels:
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dependencies:
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- conda-forge::sed=4.7

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name: rsem_merge_counts
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channels:
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dependencies:
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- conda-forge::sed=4.7

‎modules/local/star_align_igenomes/environment.yml

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name: star_align_igenomes
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channels:
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dependencies:
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- bioconda::star=2.6.1d
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- bioconda::samtools=1.10

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name: star_genomegenerate_igenomes
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channels:
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dependencies:
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- bioconda::star=2.6.1d
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- bioconda::samtools=1.10

‎modules/nf-core/bbmap/bbsplit/environment.yml

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‎modules/nf-core/bedtools/genomecov/environment.yml

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‎modules/nf-core/cat/fastq/environment.yml

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‎modules/nf-core/custom/catadditionalfasta/environment.yml

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‎modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py

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‎modules/nf-core/custom/getchromsizes/environment.yml

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‎modules/nf-core/custom/tx2gene/environment.yml

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‎modules/nf-core/custom/tx2gene/templates/tx2gene.py

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‎modules/nf-core/dupradar/environment.yml

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‎modules/nf-core/fastp/environment.yml

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‎modules/nf-core/fastqc/environment.yml

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‎modules/nf-core/fq/subsample/environment.yml

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‎modules/nf-core/gffread/environment.yml

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‎modules/nf-core/gunzip/environment.yml

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‎modules/nf-core/hisat2/align/environment.yml

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‎modules/nf-core/hisat2/align/main.nf

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‎modules/nf-core/hisat2/build/environment.yml

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‎modules/nf-core/hisat2/build/main.nf

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