nf-core · pinin4fjords · Dec 5, 2025 · Dec 5, 2025 · Dec 5, 2025 · Dec 5, 2025
diff --git 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
 

diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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",