From e7a8e178ddd8c9678f12723a534fb678ec342ad1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 5 Dec 2025 16:50:14 +0000 Subject: [PATCH 1/3] Add dupMatrix files to nftignore for reproducibility MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit DupRadar's dupMatrix output files have non-reproducible content due to conda dependency drift, causing ARM CI test failures. Adding these files to .nftignore and removing their md5 checksums from snapshot files. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- tests/.nftignore | 1 + tests/bam_input.nf.test.snap | 10 ---------- tests/default.nf.test.snap | 5 ----- tests/featurecounts_group_type.nf.test.snap | 5 ----- tests/hisat2.nf.test.snap | 5 ----- tests/min_mapped_reads.nf.test.snap | 3 --- tests/remove_ribo_rna.nf.test.snap | 5 ----- tests/sentieon_default.nf.test.snap | 5 ----- tests/skip_trimming.nf.test.snap | 5 ----- tests/star_rsem.nf.test.snap | 5 ----- tests/umi.nf.test.snap | 10 ---------- 11 files changed, 1 insertion(+), 58 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 8a0e07fc6..e1cdca35b 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -29,6 +29,7 @@ umitools/*.umi_extract.log {hisat2,star_rsem,star_salmon}/*.{bam,bam.bai} {hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig {hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf +{hisat2,star_rsem,star_salmon}/dupradar/gene_data/*_dupMatrix.txt {hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf {hisat2,star_rsem,star_salmon}/dupradar/intercepts_slope/*_intercept_slope.txt {hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 158ef53dc..37fd83852 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -890,11 +890,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,96a5cd7e86bd8435c9ddc938ef55a0fb", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1f1fe07826e1cc741628f3f144cbeb37", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,8930057b6b4d05cbc24acc4ed151962d", - "WT_REP1_dupMatrix.txt:md5,5941882e05b1ef912d903090d782188e", - "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,d5a54127f0167db3fecff466387920c0", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,b3fc7acb6a8f9b2d35dcfac76dcfdd3d", @@ -1830,11 +1825,6 @@ "RAP1_UNINDUCED_REP2.sorted.bam.bai:md5,21a49b49cd6afb56c387fb645d50c3e4", "WT_REP1.sorted.bam.bai:md5,0ddc8843704fe1fc249cf1686674d6ee", "WT_REP2.sorted.bam.bai:md5,f4d9589398b0cac3dfb3356c787ae6b5", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,b0f61cd1f59e8873ea6a959b325bd85d", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,b90f05fe745bddfa28f76d4793437d45", - "WT_REP1_dupMatrix.txt:md5,e3927c65b43c103757c62000a0e52f89", - "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,5a7a4291e8ff6cc25a4eb72dfdf06b51", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,9cf6f9377ea65e3bdb16b55992028d66", diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8b50db2cc..dd34419a7 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1419,11 +1419,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0", - "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,07bd87d86ba5c6c3ceff36518183417d", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 936a82fb2..cc4ac7946 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1384,11 +1384,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0", - "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index e4981ff1d..f2a31a64a 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1202,11 +1202,6 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8a6bf324a928534cb7ed7a5522aff7d0", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,ae3e70edc98ec8117608f8f608effab9", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c", - "WT_REP1_dupMatrix.txt:md5,11371da7a087879340c2e7e6842a5d89", - "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,cd7494b3bb12295a287f36506638f3c6", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,289e47b060051eb33c17e52aa0ce52cc", diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index c5f79c4ce..60c31655b 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1153,9 +1153,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,07bd87d86ba5c6c3ceff36518183417d", diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index dd733218e..73d64b7d3 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1338,11 +1338,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", - "WT_REP1_dupMatrix.txt:md5,b82c4fed335d03e85c414c91c2efd461", - "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,accedae963f399d3b47effd8eda41edb", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,1769902d5214f137e12f89156c5334c9", diff --git a/tests/sentieon_default.nf.test.snap b/tests/sentieon_default.nf.test.snap index cc73e9d25..3ad6572bf 100644 --- a/tests/sentieon_default.nf.test.snap +++ b/tests/sentieon_default.nf.test.snap @@ -1417,11 +1417,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,fefd4fafa0bd46c93de8da0857dd3672", - "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,07bd87d86ba5c6c3ceff36518183417d", diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 146999d00..c3d48edb6 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1202,11 +1202,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,fdeebc4f056cbb52fee53e82c2e0096f", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,aa94a148bdbebec4e82cd18a00316506", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf", - "WT_REP1_dupMatrix.txt:md5,04512c8be70c1898d0262935ed5ec5bd", - "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,bc80cee5887507179965623c3dfef4f9", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,efc257c3c0f9a9d7eabc0449bbbf0f10", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 18a53941c..fe1bcedfd 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1266,11 +1266,6 @@ "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,3f269a6b2e9c8eaab66582e31d208dfc", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa", - "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78", - "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,5a7a4291e8ff6cc25a4eb72dfdf06b51", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,9cf6f9377ea65e3bdb16b55992028d66", diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap index 6e9fe17bb..311326c63 100644 --- a/tests/umi.nf.test.snap +++ b/tests/umi.nf.test.snap @@ -1396,11 +1396,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,a3b1b764e21b500d9ffed5beb6da85ac", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,0b8c54ea7f2a78f7dd478a7bde53143e", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,ed386269dd82129149da4d33a9e0e0b6", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,ee34da4ee0f7b56c710f5df041f88f31", - "WT_REP1_dupMatrix.txt:md5,6416d48ec754942e0a5a0c1a81680fe5", - "WT_REP2_dupMatrix.txt:md5,60e583c84a0d8b31cb667703c56d6c33", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,d0e2b4a2e14fa97ad49c4baacfb1d5e3", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,3f65cd0875ee679cc608d64c42daa40a", @@ -2600,11 +2595,6 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,a32f996ee7119c10cdfc3c706fed8560", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,0f0858724747050c17a9009fe7f7827d", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,6726b1c5e63db1f6efd2882de701adc1", - "WT_REP1_dupMatrix.txt:md5,1d57d6942d0720bddd25ff260dce08fa", - "WT_REP2_dupMatrix.txt:md5,b944b0f71ef8a98b5a4d53f4542c8e6f", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,8433a395e65315feb0f8bfca4a1d1aba", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.tsv:md5,783a4395a02312e94b9f890fb9e18f6e", From e72e572342af24f79da3a7a1cdda752c0ea053be Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 5 Dec 2025 16:51:10 +0000 Subject: [PATCH 2/3] Update changelog for PR #1651 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cc1434a66..c19a837cf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ Special thanks to the following for their contributions to the release: - [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 - [PR #1650](https://github.com/nf-core/rnaseq/pull/1650) - Restrict ARM CI tests to Docker profile only +- [PR #1651](https://github.com/nf-core/rnaseq/pull/1651) - Add dupMatrix files to nftignore to fix conda reproducibility issues ## [[3.22.0](https://github.com/nf-core/rnaseq/releases/tag/3.22.0)] - 2025-11-26 From 3ffe0ee400a437dcb141cf94ad7a9acdd5de027a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 5 Dec 2025 16:52:05 +0000 Subject: [PATCH 3/3] Trigger CI