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Fix HISAT2 issues: BAM CSI index with UMI deduplication #1645

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Merged
pinin4fjords merged 6 commits into from
Dec 4, 2025
+40 −18
Merged

Fix HISAT2 issues: BAM CSI index with UMI deduplication #1645

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6fa24cf
Fix BAM CSI index access with UMI deduplication
pinin4fjords Dec 2, 2025
4e00a70
Update hisat2/align module and patch for large genome support
pinin4fjords Dec 2, 2025
0ffaccb
Add issue reporter to credits
pinin4fjords Dec 2, 2025
f1ad1e0
Prettier
pinin4fjords Dec 2, 2025
86cb8d7
Merge branch 'dev' into fix/bam-csi-index-umi-dedup
pinin4fjords Dec 3, 2025
b09e3e4
Update RSEM test snapshots for new long format output files
pinin4fjords Dec 3, 2025
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,10 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Credits

Special thanks to the following for their contributions to the release:

- [sisterdot](https://github.com/sisterdot)

### Enhancements and fixes

- [PR #1640](https://github.com/nf-core/rnaseq/pull/1640) - Bump version after release 3.22.0
- [PR #1641](https://github.com/nf-core/rnaseq/pull/1641) - Add arm-based CI tests and fix arm-related issues
- [PR #1645](https://github.com/nf-core/rnaseq/pull/1645) - Fix BAM CSI index access error with UMI deduplication ([#1643](https://github.com/nf-core/rnaseq/issues/1643))
- [PR #1642](https://github.com/nf-core/rnaseq/pull/1642) - Add long format to rsem merge

## [[3.22.0](https://github.com/nf-core/rnaseq/releases/tag/3.22.0)] - 2025-11-26
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -77,7 +77,7 @@
},
"hisat2/align": {
"branch": "master",
"git_sha": "20b042e352fc47ab6dab717a622253e96429e887",
"git_sha": "5ec0e05ebe154cf1325de4c8ae07cdff1a197b06",
"installed_by": ["fastq_align_hisat2"],
"patch": "modules/nf-core/hisat2/align/hisat2-align.diff"
},
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4 changes: 2 additions & 2 deletions modules/nf-core/hisat2/align/hisat2-align.diff
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4 changes: 2 additions & 2 deletions modules/nf-core/hisat2/align/main.nf
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31 changes: 20 additions & 11 deletions modules/nf-core/hisat2/align/meta.yml
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4 changes: 4 additions & 0 deletions tests/bam_input.nf.test.snap
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Expand Up @@ -1300,6 +1300,8 @@
"rsem/WT_REP2.transcript.bam",
"rsem/rsem.merged.gene_counts.tsv",
"rsem/rsem.merged.gene_tpm.tsv",
"rsem/rsem.merged.genes_long.tsv",
"rsem/rsem.merged.isoforms_long.tsv",
"rsem/rsem.merged.transcript_counts.tsv",
"rsem/rsem.merged.transcript_tpm.tsv",
"samtools",
Expand Down Expand Up @@ -1819,6 +1821,8 @@
"WT_REP2.transcript.bam:md5,a5f965731a3fd6e523f4960d7d462f97",
"rsem.merged.gene_counts.tsv:md5,47a75de167a1b72d3a20789df389a3f7",
"rsem.merged.gene_tpm.tsv:md5,18a6dd460737434f6da1c17c1dc8aafa",
"rsem.merged.genes_long.tsv:md5,24767425e5d9d914ed0b1eca431182ac",
"rsem.merged.isoforms_long.tsv:md5,1363e166497e4574793a9f4704841767",
"rsem.merged.transcript_counts.tsv:md5,d3a4fa1f3bde89ee9d30114af2db3b48",
"rsem.merged.transcript_tpm.tsv:md5,efa563d0402cae35b96380592d147a72",
"RAP1_IAA_30M_REP1.sorted.bam.bai:md5,4460948fc194ba7c7fe7ad92e68132a0",
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4 changes: 4 additions & 0 deletions tests/star_rsem.nf.test.snap
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Expand Up @@ -986,6 +986,8 @@
"star_rsem/qualimap/WT_REP2/rnaseq_qc_results.txt",
"star_rsem/rsem.merged.gene_counts.tsv",
"star_rsem/rsem.merged.gene_tpm.tsv",
"star_rsem/rsem.merged.genes_long.tsv",
"star_rsem/rsem.merged.isoforms_long.tsv",
"star_rsem/rsem.merged.transcript_counts.tsv",
"star_rsem/rsem.merged.transcript_tpm.tsv",
"star_rsem/rseqc",
Expand Down Expand Up @@ -1306,6 +1308,8 @@
"coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846",
"rsem.merged.gene_counts.tsv:md5,990cdaf5071c9bfd3d2d99296feb68f3",
"rsem.merged.gene_tpm.tsv:md5,349f2184161d6b269a0f5c4da1dee07a",
"rsem.merged.genes_long.tsv:md5,42e9a0220b0e3a505d7b59df279ce89a",
"rsem.merged.isoforms_long.tsv:md5,8c6f65b49b920e48caf93dc04e1a546c",
"rsem.merged.transcript_counts.tsv:md5,3ca2bb5c22438e0bd104c9d052bc8241",
"rsem.merged.transcript_tpm.tsv:md5,f59e35398f30d49875e41bcc03d082ed",
"RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de",
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4 changes: 2 additions & 2 deletions workflows/rnaseq/main.nf
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Expand Up @@ -253,7 +253,7 @@ workflow RNASEQ {

ch_genome_bam = BAM_DEDUP_UMI_STAR.out.bam
ch_transcriptome_bam = BAM_DEDUP_UMI_STAR.out.transcriptome_bam
ch_genome_bam_index = params.bam_csi_index ? BAM_DEDUP_UMI_STAR.out.csi : BAM_DEDUP_UMI_STAR.out.bai
ch_genome_bam_index = BAM_DEDUP_UMI_STAR.out.bai
ch_versions = ch_versions.mix(BAM_DEDUP_UMI_STAR.out.versions)

ch_multiqc_files = ch_multiqc_files
Expand Down Expand Up @@ -359,7 +359,7 @@ workflow RNASEQ {
)

ch_genome_bam = BAM_DEDUP_UMI_HISAT2.out.bam
ch_genome_bam_index = params.bam_csi_index ? BAM_DEDUP_UMI_HISAT2.out.csi : BAM_DEDUP_UMI_HISAT2.out.bai
ch_genome_bam_index = BAM_DEDUP_UMI_HISAT2.out.bai
ch_versions = ch_versions.mix(BAM_DEDUP_UMI_HISAT2.out.versions)

ch_multiqc_files = ch_multiqc_files
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