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Merge pull request #1212 from maxulysse/update_modules
CHORES: Update all modules
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‎CHANGELOG.md

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@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch)
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- [PR #1201](https://github.com/nf-core/rnaseq/pull/1201) - Template update for nf-core/tools v2.12
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- [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config`
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- [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
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### Parameters
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‎modules.json

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},
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"rsem/calculateexpression": {
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"branch": "master",
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"git_sha": "8ec12d844837b0167540c910afe4d3f920cd7114",
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"git_sha": "7c82eda52cb493c4cf500e3fb7d1597a5d766165",
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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": "8ec12d844837b0167540c910afe4d3f920cd7114",
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"git_sha": "301b088c7e9e00c4c80686411383f07173b54d69",
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"installed_by": ["modules"]
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},
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"rseqc/bamstat": {
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"branch": "master",
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"git_sha": "41f4baa439663b9027727d83a3293db93bad3f8c",
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"git_sha": "9eb22e4d3f28c274b7c498a1564581377349a242",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/inferexperiment": {
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},
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"rseqc/readdistribution": {
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"branch": "master",
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"git_sha": "41f4baa439663b9027727d83a3293db93bad3f8c",
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"git_sha": "d5f5ce9474983fe0973b26c39728b5c57b13c8d4",
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"installed_by": ["bam_rseqc"]
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},
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"rseqc/readduplication": {
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},
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"rseqc/tin": {
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"branch": "master",
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"git_sha": "41f4baa439663b9027727d83a3293db93bad3f8c",
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"git_sha": "37aa78c23d809a01d6a1f2e6c0c034f00c2a0984",
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"installed_by": ["bam_rseqc"]
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},
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"salmon/index": {
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"branch": "master",
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"git_sha": "ce801ced94947b2ff01002b4120eef2f79489b34",
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"git_sha": "ffc101e1b84ef3df2e4e4a966e84b3c513ae5693",
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"installed_by": ["fastq_subsample_fq_salmon"]
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},
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"salmon/quant": {
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"branch": "master",
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"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
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"git_sha": "ffc101e1b84ef3df2e4e4a966e84b3c513ae5693",
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"installed_by": ["fastq_subsample_fq_salmon", "modules"]
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "8d8f0ae52d6c9342bd41c33dda0b74b07e32153d",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "8d8f0ae52d6c9342bd41c33dda0b74b07e32153d",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "8d8f0ae52d6c9342bd41c33dda0b74b07e32153d",
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"installed_by": [
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"bam_dedup_stats_samtools_umitools",
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"bam_markduplicates_picard",
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "8d8f0ae52d6c9342bd41c33dda0b74b07e32153d",
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"installed_by": ["bam_sort_stats_samtools"]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
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"git_sha": "8d8f0ae52d6c9342bd41c33dda0b74b07e32153d",
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"installed_by": ["bam_stats_samtools"]
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},
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"sortmerna": {
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"branch": "master",
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"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
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"git_sha": "ad22467dff16284093e7335d5e77964e9bbc510b",
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"installed_by": ["modules"]
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},
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"star/align": {
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"branch": "master",
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"git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e",
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"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
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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": "1e2b7fb7106852388610c0360d234b0829eb980e",
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"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
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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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"git_sha": "b0dcb44b018d9b2bcb35b1abb7bcd34061bc5a6d",
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"git_sha": "5756b12b1fab0c07f05b9ad2d5d5c262b1a2c1ef",
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"installed_by": ["modules"]
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},
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"subread/featurecounts": {
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"branch": "master",
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"git_sha": "d062b356938ea98d29b298691adf0620d3c3bdf0",
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"git_sha": "f6bba1a67cdbb605f24d7a4e8dd383b0eec45b52",
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"installed_by": ["modules"]
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},
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"trimgalore": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"git_sha": "2e6c468e0ad43b23df71d7a7f130d5c0e0aa89e3",
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"installed_by": ["fastq_fastqc_umitools_trimgalore"]
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},
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"ucsc/bedclip": {
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"branch": "master",
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"git_sha": "8899867378857ade0a68d1e6744619070ccbc2d4",
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"git_sha": "7c75d01997236f61b9b77399d9933cb36041f2c3",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"ucsc/bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"git_sha": "7c75d01997236f61b9b77399d9933cb36041f2c3",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"umitools/dedup": {
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},
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"umitools/extract": {
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"branch": "master",
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"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
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"git_sha": "9e56d7a647fbf6f7e45ef123bc916ad66b6f7c9d",
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"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
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},
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"untar": {
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},
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"bam_rseqc": {
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"branch": "master",
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"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
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"git_sha": "9eb22e4d3f28c274b7c498a1564581377349a242",
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"installed_by": ["subworkflows"]
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},
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"bam_sort_stats_samtools": {
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},
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"utils_nfcore_pipeline": {
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"branch": "master",
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"git_sha": "73b63c8e510107010ab13b68cf31189d6cdca8cb",
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"git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
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"installed_by": ["subworkflows"]
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},
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"utils_nfvalidation_plugin": {

‎modules/nf-core/rsem/calculateexpression/tests/main.nf.test

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‎modules/nf-core/rsem/preparereference/tests/main.nf.test

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‎modules/nf-core/rseqc/bamstat/tests/main.nf.test

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‎modules/nf-core/rseqc/bamstat/tests/main.nf.test.snap

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‎modules/nf-core/rseqc/readdistribution/tests/main.nf.test

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‎modules/nf-core/rseqc/readdistribution/tests/main.nf.test.snap

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‎modules/nf-core/rseqc/tin/tests/main.nf.test

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‎modules/nf-core/rseqc/tin/tests/main.nf.test.snap

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‎modules/nf-core/salmon/index/tests/main.nf.test

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‎modules/nf-core/salmon/index/tests/main.nf.test.snap

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