update a couple more snaps

Author: pinin4fjords

tests/min_mapped_reads.nf.test.snap

@@ -213,6 +213,7 @@
                 "multiqc/star_salmon",
                 "multiqc/star_salmon/multiqc_report.html",
                 "multiqc/star_salmon/multiqc_report_data",
+                "multiqc/star_salmon/multiqc_report_data/BETA-multiqc.parquet",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
@@ -291,8 +292,8 @@
                 "multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt",
                 "multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/salmon_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt",
-                "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-pct-table.txt",
+                "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-table.txt",
                 "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt",
@@ -335,7 +336,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf",
@@ -358,8 +358,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf",
@@ -406,7 +406,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png",
@@ -429,8 +428,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png",
@@ -477,7 +476,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg",
@@ -500,8 +498,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg",
@@ -1148,9 +1146,6 @@
                 "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",
@@ -1194,9 +1189,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-05-02T19:13:23.557869665"
+        "timestamp": "2025-06-03T18:47:21.80848308"
     },
     "Params: --min_mapped_reads 90 - stub": {
         "content": [

tests/skip_qc.nf.test.snap

@@ -726,8 +726,6 @@
                 "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "samtools-flagstat-pct-table.txt:md5,616aa1d4a2302449198250143dcf1ed1",
-                "samtools-flagstat-table.txt:md5,f44d31d9f43141527cc096ff112d3827",
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8",
@@ -819,6 +817,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-06-03T15:59:00.769625008"
+        "timestamp": "2025-06-03T18:32:24.98419919"
     }
-}
+}