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Merge pull request #1558 from nf-core/remove_patches
Remove patches and bump modules for ARM compat
2 parents 21acf5a + 0ee54ba commit a60f6cf

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‎CHANGELOG.md‎

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@@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [PR #1550](https://github.com/nf-core/rnaseq/pull/1550) - Simplify `SummarizedExperiment` outputs.
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- [PR #1553](https://github.com/nf-core/rnaseq/pull/1553) - Make jobs automatically resubmit for exit code 175
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- [PR #1556](https://github.com/nf-core/rnaseq/pull/1556) - Update index docs to remove references to 'indexing only mode'
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- [PR #1558](https://github.com/nf-core/rnaseq/pull/1558) - Remove patches and bump modules for ARM compat
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# 3.18.0 - 2024-12-19
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‎conf/arm.config‎

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‎main.nf‎

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@@ -117,8 +117,7 @@ workflow NFCORE_RNASEQ {
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PREPARE_GENOME.out.bbsplit_index,
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PREPARE_GENOME.out.rrna_fastas,
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PREPARE_GENOME.out.sortmerna_index,
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PREPARE_GENOME.out.splicesites,
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!params.remove_ribo_rna && params.remove_ribo_rna
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PREPARE_GENOME.out.splicesites
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)
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ch_versions = ch_versions.mix(RNASEQ.out.versions)
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‎modules.json‎

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},
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"bracken/bracken": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
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"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
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"patch": "modules/nf-core/cat/fastq/cat-fastq.diff"
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"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
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},
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"custom/catadditionalfasta": {
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"branch": "master",
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},
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"hisat2/align": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["fastq_align_hisat2"],
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"patch": "modules/nf-core/hisat2/align/hisat2-align.diff"
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},
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"hisat2/build": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["modules"]
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},
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"hisat2/extractsplicesites": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["modules"]
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},
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"kallisto/index": {
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},
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"kraken2/kraken2": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
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"git_sha": "471cf3ca1617271b9b6fea09ea2ebdee78b874de",
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"installed_by": ["modules"]
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},
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"picard/markduplicates": {
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},
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"rsem/calculateexpression": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["modules"]
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},
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"rsem/preparereference": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["modules"]
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},
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"rseqc/bamstat": {
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},
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"sortmerna": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"],
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"patch": "modules/nf-core/sortmerna/sortmerna.diff"
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"git_sha": "d4a425ce59fc803a11e520f16680ede9af09761f",
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"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
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},
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"star/align": {
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"branch": "master",
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"git_sha": "3c259f0ac1ed9ae3f6b835461d054edffc60120e",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/star/align/star-align.diff"
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"installed_by": ["modules"]
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},
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"star/genomegenerate": {
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"branch": "master",
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"git_sha": "3c259f0ac1ed9ae3f6b835461d054edffc60120e",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff"
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"installed_by": ["modules"]
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},
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"stringtie/stringtie": {
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"branch": "master",
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},
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"fastq_align_hisat2": {
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"branch": "master",
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"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
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"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
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"installed_by": ["subworkflows"]
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},
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"fastq_fastqc_umitools_fastp": {
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},
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"fastq_qc_trim_filter_setstrandedness": {
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"branch": "master",
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"git_sha": "a9d1fd8afc427ddc5222c0a0774cb459170005a1",
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"git_sha": "db5a84497b80c4932b4498ec231f19403d19bcff",
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"installed_by": ["subworkflows"]
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},
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"fastq_subsample_fq_salmon": {

‎modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff‎

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‎modules/nf-core/bracken/bracken/environment.yml‎

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‎modules/nf-core/bracken/bracken/main.nf‎

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‎modules/nf-core/bracken/bracken/tests/main.nf.test‎

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‎modules/nf-core/bracken/bracken/tests/main.nf.test.snap‎

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‎modules/nf-core/cat/fastq/cat-fastq.diff‎

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