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fix some more snaps
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3 files changed

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-46
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‎tests/hisat2.nf.test.snap‎

Lines changed: 12 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -156,7 +156,7 @@
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},
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"HISAT2_ALIGN": {
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"hisat2": "2.2.1",
159-
"samtools": "1.16.1"
159+
"samtools": 1.2
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},
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"HISAT2_EXTRACTSPLICESITES": {
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"hisat2": "2.2.1"
@@ -784,6 +784,7 @@
784784
"multiqc/hisat2",
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"multiqc/hisat2/multiqc_report.html",
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"multiqc/hisat2/multiqc_report_data",
787+
"multiqc/hisat2/multiqc_report_data/BETA-multiqc.parquet",
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"multiqc/hisat2/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
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"multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
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"multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
@@ -861,8 +862,8 @@
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"multiqc/hisat2/multiqc_report_data/rseqc_read_dups.txt",
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"multiqc/hisat2/multiqc_report_data/rseqc_read_dups_plot.txt",
863864
"multiqc/hisat2/multiqc_report_data/salmon_plot.txt",
864-
"multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt",
865-
"multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt",
865+
"multiqc/hisat2/multiqc_report_data/samtools-flagstat-pct-table.txt",
866+
"multiqc/hisat2/multiqc_report_data/samtools-flagstat-table.txt",
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"multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt",
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"multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt",
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"multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt",
@@ -902,7 +903,6 @@
902903
"multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf",
@@ -929,8 +929,8 @@
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"multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/salmon_plot.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/sample-relationships.pdf",
932-
"multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
933-
"multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
932+
"multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf",
933+
"multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-table.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf",
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"multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf",
@@ -973,7 +973,6 @@
973973
"multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
974974
"multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
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"multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
976-
"multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png",
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"multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png",
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"multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png",
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"multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png",
@@ -1000,8 +999,8 @@
1000999
"multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png",
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"multiqc/hisat2/multiqc_report_plots/png/salmon_plot.png",
10021001
"multiqc/hisat2/multiqc_report_plots/png/sample-relationships.png",
1003-
"multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
1004-
"multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
1002+
"multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-pct-table.png",
1003+
"multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-table.png",
10051004
"multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
10061005
"multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png",
10071006
"multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png",
@@ -1044,7 +1043,6 @@
10441043
"multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
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"multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
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"multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
1047-
"multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg",
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"multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg",
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"multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg",
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"multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg",
@@ -1071,8 +1069,8 @@
10711069
"multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
10721070
"multiqc/hisat2/multiqc_report_plots/svg/salmon_plot.svg",
10731071
"multiqc/hisat2/multiqc_report_plots/svg/sample-relationships.svg",
1074-
"multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
1075-
"multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
1072+
"multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg",
1073+
"multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-table.svg",
10761074
"multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
10771075
"multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg",
10781076
"multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg",
@@ -1207,11 +1205,6 @@
12071205
"RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c",
12081206
"WT_REP1_dupMatrix.txt:md5,11371da7a087879340c2e7e6842a5d89",
12091207
"WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0",
1210-
"RAP1_IAA_30M_REP1_intercept_slope.txt:md5,1285c70833b46849b726412858736ed7",
1211-
"RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a2efe7c3cad6f910d5dc208c2825a245",
1212-
"RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9",
1213-
"WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873",
1214-
"WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2",
12151208
"RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,cd7494b3bb12295a287f36506638f3c6",
12161209
"RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
12171210
"RAP1_IAA_30M_REP1.featureCounts.txt:md5,a60088d7013eebeb240e02457431eedb",
@@ -1342,8 +1335,8 @@
13421335
],
13431336
"meta": {
13441337
"nf-test": "0.9.2",
1345-
"nextflow": "24.10.6"
1338+
"nextflow": "25.04.2"
13461339
},
1347-
"timestamp": "2025-05-02T18:55:20.186245374"
1340+
"timestamp": "2025-06-03T17:40:30.487659861"
13481341
}
13491342
}

‎tests/remove_ribo_rna.nf.test.snap‎

Lines changed: 2 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1267,8 +1267,6 @@
12671267
"qualimap_gene_coverage_profile_Normalised.txt:md5,3297068282f57506f40070b8bc6ad1b5",
12681268
"qualimap_rnaseq_cov_hist.txt:md5,a523cfcb52fe8f2d5902d933568a790d",
12691269
"rseqc_infer_experiment_plot.txt:md5,d8741451248f1a5a4ebe3230c1af9c95",
1270-
"samtools-flagstat-pct-table.txt:md5,811c13b6c26200f0507149247dd03404",
1271-
"samtools-flagstat-table.txt:md5,f6de841b5c18f6b29417ecc8869948af",
12721270
"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
12731271
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72",
12741272
"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,4ff26c0457ddceb4a03e874222b46f00",
@@ -1335,11 +1333,6 @@
13351333
"RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc",
13361334
"WT_REP1_dupMatrix.txt:md5,b82c4fed335d03e85c414c91c2efd461",
13371335
"WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677",
1338-
"RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d",
1339-
"RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695",
1340-
"RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b0cbd0122c0fc5dd1821450eb41ba577",
1341-
"WT_REP1_intercept_slope.txt:md5,7db7a898152e8eaab96b1aaf0e567e50",
1342-
"WT_REP2_intercept_slope.txt:md5,c16fb72dbde510dc74ac0286b635d0aa",
13431336
"RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,accedae963f399d3b47effd8eda41edb",
13441337
"RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
13451338
"RAP1_IAA_30M_REP1.featureCounts.txt:md5,e37ededa12690a8ccae2eb42dac47ed6",
@@ -1407,7 +1400,7 @@
14071400
"nf-test": "0.9.2",
14081401
"nextflow": "25.04.2"
14091402
},
1410-
"timestamp": "2025-06-03T13:08:56.053404337"
1403+
"timestamp": "2025-06-03T18:18:03.365506226"
14111404
},
14121405
"Params: --remove_ribo_rna - stub": {
14131406
"content": [
@@ -1516,4 +1509,4 @@
15161509
},
15171510
"timestamp": "2025-06-03T13:10:09.375619385"
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}
1519-
}
1512+
}

‎tests/skip_trimming.nf.test.snap‎

Lines changed: 11 additions & 18 deletions
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@@ -185,6 +185,7 @@
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"multiqc/star_salmon",
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"multiqc/star_salmon/multiqc_report.html",
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"multiqc/star_salmon/multiqc_report_data",
188+
"multiqc/star_salmon/multiqc_report_data/BETA-multiqc.parquet",
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"multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
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"multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
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"multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
@@ -246,8 +247,8 @@
246247
"multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt",
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"multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt",
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"multiqc/star_salmon/multiqc_report_data/salmon_plot.txt",
249-
"multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt",
250-
"multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt",
250+
"multiqc/star_salmon/multiqc_report_data/samtools-flagstat-pct-table.txt",
251+
"multiqc/star_salmon/multiqc_report_data/samtools-flagstat-table.txt",
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"multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt",
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"multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt",
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"multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt",
@@ -273,7 +274,6 @@
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"multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf",
@@ -296,8 +296,8 @@
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"multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
299-
"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
300-
"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
299+
"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf",
300+
"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-table.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf",
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"multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf",
@@ -327,7 +327,6 @@
327327
"multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
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"multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
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"multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
330-
"multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
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"multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png",
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"multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png",
333332
"multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png",
@@ -350,8 +349,8 @@
350349
"multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
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"multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
352351
"multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
353-
"multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
354-
"multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
352+
"multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-pct-table.png",
353+
"multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-table.png",
355354
"multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
356355
"multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png",
357356
"multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png",
@@ -381,7 +380,6 @@
381380
"multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
382381
"multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
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"multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
384-
"multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
385383
"multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg",
386384
"multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg",
387385
"multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg",
@@ -404,8 +402,8 @@
404402
"multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
405403
"multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
406404
"multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
407-
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
408-
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
405+
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg",
406+
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-table.svg",
409407
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
410408
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg",
411409
"multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg",
@@ -1199,11 +1197,6 @@
11991197
"RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf",
12001198
"WT_REP1_dupMatrix.txt:md5,04512c8be70c1898d0262935ed5ec5bd",
12011199
"WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1",
1202-
"RAP1_IAA_30M_REP1_intercept_slope.txt:md5,7962ee6ba989f9af6465aaf1101ba13b",
1203-
"RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,6c69ccc819c14847eef319b7fa8ccb4f",
1204-
"RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612",
1205-
"WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297",
1206-
"WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41",
12071200
"RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,bc80cee5887507179965623c3dfef4f9",
12081201
"RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
12091202
"RAP1_IAA_30M_REP1.featureCounts.txt:md5,b1ed22e51a94a0ca8f030ff4e09295aa",
@@ -1269,8 +1262,8 @@
12691262
],
12701263
"meta": {
12711264
"nf-test": "0.9.2",
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"nextflow": "24.10.6"
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"nextflow": "25.04.2"
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},
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"timestamp": "2025-05-02T19:57:03.409484347"
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"timestamp": "2025-06-03T17:56:51.374055108"
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}
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}

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