update .nftignore and snapshots

maxulysse · maxulysse · commit 6afadbb77c40 · 2025-06-03T18:39:51.000+02:00
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -18,6 +18,7 @@ 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/intercepts_slope/*_intercept_slope.txt
 {hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf
 {hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf
 {hisat2,star_rsem,star_salmon}/featurecounts/*.featureCounts.txt.summary
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -1419,11 +1419,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
                 "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0",
                 "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
-                "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898",
-                "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
                 "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.txt:md5,2a5c8c10f4371048d7d459411b58b087",
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -1384,11 +1384,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
                 "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0",
                 "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
-                "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898",
-                "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
                 "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
@@ -1207,11 +1207,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c",
                 "WT_REP1_dupMatrix.txt:md5,11371da7a087879340c2e7e6842a5d89",
                 "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,1285c70833b46849b726412858736ed7",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a2efe7c3cad6f910d5dc208c2825a245",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9",
-                "WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873",
-                "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2",
                 "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.txt:md5,a60088d7013eebeb240e02457431eedb",
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -1148,9 +1148,6 @@
                 "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_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
                 "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.txt:md5,2a5c8c10f4371048d7d459411b58b087",
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -1335,11 +1335,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc",
                 "WT_REP1_dupMatrix.txt:md5,b82c4fed335d03e85c414c91c2efd461",
                 "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217",
-                "WT_REP1_intercept_slope.txt:md5,7db7a898152e8eaab96b1aaf0e567e50",
-                "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2",
                 "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.txt:md5,e37ededa12690a8ccae2eb42dac47ed6",
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -1199,11 +1199,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf",
                 "WT_REP1_dupMatrix.txt:md5,04512c8be70c1898d0262935ed5ec5bd",
                 "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,7962ee6ba989f9af6465aaf1101ba13b",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,6c69ccc819c14847eef319b7fa8ccb4f",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612",
-                "WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297",
-                "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41",
                 "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.txt:md5,b1ed22e51a94a0ca8f030ff4e09295aa",
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -1224,11 +1224,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa",
                 "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78",
                 "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,d280fe126a5e82d24121d8662fd5a161",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a498640b0f9e710311ebc3eb67cedbd0",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e",
-                "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965",
-                "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c",
                 "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.txt:md5,a8200ec76e7916dc1210447130f77bbf",
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
@@ -1397,11 +1397,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,ee34da4ee0f7b56c710f5df041f88f31",
                 "WT_REP1_dupMatrix.txt:md5,6416d48ec754942e0a5a0c1a81680fe5",
                 "WT_REP2_dupMatrix.txt:md5,60e583c84a0d8b31cb667703c56d6c33",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,6c1e7c494f765ff6466ab023d52a1d70",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,93a525d3bc1ebfeddc8f04f3c2238237",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,74f6210123d50c2001f20dad6283e856",
-                "WT_REP1_intercept_slope.txt:md5,4d428c55745bf9e2832d7fdb76b72088",
-                "WT_REP2_intercept_slope.txt:md5,d6a47171cb52331c5e6e21671152fb98",
                 "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.txt:md5,c90762d8ee1df9219dc643b68e464ca0",
@@ -2604,11 +2599,6 @@
                 "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,6726b1c5e63db1f6efd2882de701adc1",
                 "WT_REP1_dupMatrix.txt:md5,1d57d6942d0720bddd25ff260dce08fa",
                 "WT_REP2_dupMatrix.txt:md5,b944b0f71ef8a98b5a4d53f4542c8e6f",
-                "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,a07fbfcbd487003cdd2123cb89209d14",
-                "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,38cea811141edcfd28d1e7770628f6c9",
-                "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b897caec80a37ace72c156ed091acbcd",
-                "WT_REP1_intercept_slope.txt:md5,9895ef03e6f9282b11c4a32fe16a25b0",
-                "WT_REP2_intercept_slope.txt:md5,6c22669508aecfdfe5583c38496db314",
                 "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.txt:md5,1ecf699b693201b29cadd187bb0f2971",
