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Fix up pipeline tests
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6 files changed

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‎tests/default.nf.test.snap‎

Lines changed: 22 additions & 22 deletions
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@@ -31,8 +31,8 @@
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"gunzip": 1.1
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},
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"STAR_GENOMEGENERATE": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"star": "2.7.11b",
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"samtools": 1.2,
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"gawk": "5.1.0"
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},
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"TRIMGALORE": {
@@ -90,7 +90,7 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:18:53.239557126"
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"timestamp": "2024-10-21T18:47:30.454374101"
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},
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"Params: default": {
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"content": [
@@ -195,13 +195,13 @@
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"bioconductor-summarizedexperiment": "1.32.0"
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},
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"STAR_ALIGN": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"star": "2.7.11b",
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"samtools": 1.2,
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"gawk": "5.1.0"
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},
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"STAR_GENOMEGENERATE": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"star": "2.7.11b",
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"samtools": 1.2,
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"gawk": "5.1.0"
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},
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"STRINGTIE_STRINGTIE": {
@@ -1312,18 +1312,18 @@
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"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
1315-
"multiqc_featurecounts_biotype_plot.txt:md5,cdf1c096e3a9ecb0c1eecfd1f3b2e895",
1316-
"multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
1315+
"multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d",
1316+
"multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
1320-
"qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049",
1321-
"qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa",
1322-
"qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce",
1320+
"qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882",
1321+
"qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5",
1322+
"qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405",
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"rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218",
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"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
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"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
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"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
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"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8",
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"ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
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"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
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"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1385,12 +1385,12 @@
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"RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217",
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"RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370",
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"RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
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"WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00",
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"WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0",
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"WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
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"RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
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"RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
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"RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
1393-
"WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef",
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"WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898",
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"WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
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"RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466",
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"RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
@@ -1401,9 +1401,9 @@
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"RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4",
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"RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0",
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"RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450",
1404-
"WT_REP1.biotype_counts_mqc.tsv:md5,e0dbe5dcff076b97775677fd64b29b04",
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"WT_REP1.biotype_counts_mqc.tsv:md5,3d9d1dca4551ff5689f36ba3f23848f2",
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"WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9",
1406-
"WT_REP1.featureCounts.txt:md5,b2a80018f38c142a936e8ad5d24059f8",
1406+
"WT_REP1.featureCounts.txt:md5,e64f59d719d21293627717beb76beaf5",
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"WT_REP2.biotype_counts_mqc.tsv:md5,5cb8f29f175d07b3d8f8464bf8fcd82b",
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"WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
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"WT_REP2.featureCounts.txt:md5,0f3ed14df2ca681161c63aed8e6a7c7c",
@@ -1421,9 +1421,9 @@
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"coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
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"coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
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"coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
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"coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1",
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"coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211",
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"coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211",
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"coverage_profile_along_genes_(high).txt:md5,3863e6277dc95e3fac3f9cd5095a08eb",
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"coverage_profile_along_genes_(low).txt:md5,df84b2f592a0f02310096a2dd053397d",
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"coverage_profile_along_genes_(total).txt:md5,df84b2f592a0f02310096a2dd053397d",
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"coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3",
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"coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b",
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"coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b",
@@ -1445,7 +1445,7 @@
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"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
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"i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e",
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"e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
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"e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d",
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"e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa",
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"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
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"i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8",
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"e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
@@ -1459,6 +1459,6 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:17:50.647397994"
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"timestamp": "2024-10-21T19:14:46.845308285"
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}
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}

‎tests/featurecounts_group_type.nf.test.snap‎

Lines changed: 19 additions & 19 deletions
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"gunzip": 1.1
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},
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"STAR_GENOMEGENERATE": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"star": "2.7.11b",
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"samtools": 1.2,
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"gawk": "5.1.0"
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},
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"TRIMGALORE": {
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:32:05.21244727"
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"timestamp": "2024-10-21T18:52:01.516368536"
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},
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"Params: --featurecounts_group_type false": {
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"content": [
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"bioconductor-summarizedexperiment": "1.32.0"
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},
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"STAR_ALIGN": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"star": "2.7.11b",
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"samtools": 1.2,
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},
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"STAR_GENOMEGENERATE": {
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},
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"STRINGTIE_STRINGTIE": {
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"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
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"multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049",
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"qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa",
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"qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce",
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"qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882",
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"qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5",
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"qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405",
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"rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218",
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"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
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"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
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"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
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"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8",
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"ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
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"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
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"RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217",
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"RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370",
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"RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b",
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"WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00",
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"WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0",
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"WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5",
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"RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79",
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"RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b",
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"RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
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"WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef",
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"WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898",
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"WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
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"RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
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"RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
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"coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
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"coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
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"coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211",
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"coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211",
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"coverage_profile_along_genes_(high).txt:md5,3863e6277dc95e3fac3f9cd5095a08eb",
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"coverage_profile_along_genes_(low).txt:md5,df84b2f592a0f02310096a2dd053397d",
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"coverage_profile_along_genes_(total).txt:md5,df84b2f592a0f02310096a2dd053397d",
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"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
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"i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e",
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"e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
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"e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d",
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"e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa",
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"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
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"e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69",
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:31:07.10284645"
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"timestamp": "2024-10-21T19:24:36.371474446"
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}
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}

‎tests/min_mapped_reads.nf.test.snap‎

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"bioconductor-summarizedexperiment": "1.32.0"
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},
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"STAR_ALIGN": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"STAR_GENOMEGENERATE": {
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"STRINGTIE_STRINGTIE": {
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476",
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"multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
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"multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
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"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
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"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
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"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8",
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"ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
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"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
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"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:58:09.750638828"
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"timestamp": "2024-10-21T19:45:32.241828903"
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},
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"Params: --min_mapped_reads 90 - stub": {
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"content": [
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"gunzip": 1.1
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},
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"STAR_GENOMEGENERATE": {
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"star": "2.7.10a",
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"samtools": 1.18,
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"star": "2.7.11b",
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"samtools": 1.2,
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"gawk": "5.1.0"
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},
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"TRIMGALORE": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:59:03.576783452"
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"timestamp": "2024-10-21T19:46:21.485818867"
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}
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}

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