more snaps updated

Author: pinin4fjords

tests/featurecounts_group_type.nf.test.snap

@@ -99,9 +99,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-28T13:38:47.824968389"
+        "timestamp": "2025-06-03T19:34:02.430509936"
     },
     "Params: --featurecounts_group_type false": {
         "content": [
@@ -311,6 +311,7 @@
                 "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",
@@ -387,8 +388,8 @@
                 "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",
@@ -428,7 +429,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.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",
@@ -451,8 +451,8 @@
                 "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",
@@ -496,7 +496,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.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",
@@ -519,8 +518,8 @@
                 "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",
@@ -564,7 +563,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.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",
@@ -587,8 +585,8 @@
                 "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",
@@ -1384,11 +1382,6 @@
                 "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",
@@ -1439,8 +1432,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-05-02T18:43:19.966299161"
+        "timestamp": "2025-06-03T19:32:53.288039672"
     }
 }

tests/star_rsem.nf.test.snap

@@ -213,6 +213,7 @@
                 "multiqc/star_rsem",
                 "multiqc/star_rsem/multiqc_report.html",
                 "multiqc/star_rsem/multiqc_report_data",
+                "multiqc/star_rsem/multiqc_report_data/BETA-multiqc.parquet",
                 "multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
@@ -292,8 +293,8 @@
                 "multiqc/star_rsem/multiqc_report_data/rseqc_read_dups.txt",
                 "multiqc/star_rsem/multiqc_report_data/rseqc_read_dups_plot.txt",
                 "multiqc/star_rsem/multiqc_report_data/salmon_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt",
-                "multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt",
+                "multiqc/star_rsem/multiqc_report_data/samtools-flagstat-pct-table.txt",
+                "multiqc/star_rsem/multiqc_report_data/samtools-flagstat-table.txt",
                 "multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt",
                 "multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt",
                 "multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt",
@@ -333,7 +334,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-pct.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf",
@@ -359,8 +359,8 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/sample-relationships.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-pct-table.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf",
@@ -403,7 +403,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-pct.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png",
@@ -429,8 +428,8 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/sample-relationships.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-pct-table.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png",
@@ -473,7 +472,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-pct.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg",
@@ -499,8 +497,8 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/sample-relationships.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-pct-table.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg",
@@ -1224,11 +1222,6 @@
                 "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",
@@ -1292,13 +1285,13 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-05-02T20:07:25.787433287"
+        "timestamp": "2025-06-03T19:12:10.649620052"
     },
     "Params: --aligner star_rsem - stub": {
         "content": [
-            27,
+            26,
             {
                 "BBMAP_BBSPLIT": {
                     "bbmap": 39.1
@@ -1370,11 +1363,6 @@
                 "fq_lint/raw/RAP1_UNINDUCED_REP2.fq_lint.txt",
                 "fq_lint/raw/WT_REP1.fq_lint.txt",
                 "fq_lint/raw/WT_REP2.fq_lint.txt",
-                "multiqc",
-                "multiqc/star_rsem",
-                "multiqc/star_rsem/multiqc_data",
-                "multiqc/star_rsem/multiqc_plots",
-                "multiqc/star_rsem/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
                 "trimgalore",
@@ -1394,8 +1382,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-28T14:46:52.666136139"
+        "timestamp": "2025-06-03T19:13:26.589673682"
     }
 }