Merge pull request #1499 from nf-core/bump_multiqc

Bump MultiQC module to 1.27
nf-core · Jan 30, 2025 · f875cab · f875cab
2 parents 6069089 + 4a355a7
commit f875cab
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1482](https://github.com/nf-core/rnaseq/pull/1482) - Update trimgalore module for save_unpaired fix
 - [PR #1486](https://github.com/nf-core/rnaseq/pull/1486) - Bump STAR build for multiprocessing fix
 - [PR #1490](https://github.com/nf-core/rnaseq/pull/1490) - Make genomic FASTA input optional
+- [PR #1499](https://github.com/nf-core/rnaseq/pull/1499) - Bump MultiQC module to 1.27
 
 # 3.18.0 - 2024-12-19
 

diff --git a/modules.json b/modules.json
@@ -110,7 +110,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {

diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -98,10 +98,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T12:26:32.825018567"
+        "timestamp": "2025-01-28T13:26:07.890871152"
     },
     "Params: default": {
         "content": [
@@ -367,10 +367,10 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt",
@@ -1346,11 +1346,11 @@
                 "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
-                "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d",
+                "multiqc_featurecounts_biotype_plot.txt:md5,fb9db2fca737fbdcd1a921e683805d77",
                 "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
-                "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882",
                 "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5",
                 "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405",
@@ -1490,9 +1490,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T12:39:04.406597796"
+        "timestamp": "2025-01-28T13:24:46.099038947"
     }
-}
+}
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -98,10 +98,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:26:42.742119846"
+        "timestamp": "2025-01-28T13:38:47.824968389"
     },
     "Params: --featurecounts_group_type false": {
         "content": [
@@ -360,10 +360,10 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt",
@@ -1313,9 +1313,9 @@
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
                 "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
-                "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882",
                 "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5",
                 "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405",
@@ -1440,9 +1440,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:25:47.179044158"
+        "timestamp": "2025-01-28T13:38:00.766111515"
     }
-}
+}
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -99,10 +99,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:39:53.585492305"
+        "timestamp": "2025-01-28T13:46:14.476085587"
     },
     "Params: --aligner hisat2": {
         "content": [
@@ -834,10 +834,10 @@
                 "multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_sources.txt",
+                "multiqc/hisat2/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/hisat2/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/hisat2/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/hisat2/multiqc_report_data/picard_deduplication.txt",
-                "multiqc/hisat2/multiqc_report_data/picard_histogram.txt",
-                "multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt",
-                "multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt",
                 "multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt",
                 "multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt",
                 "multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt",
@@ -1293,11 +1293,11 @@
                 "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
-                "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e",
+                "multiqc_featurecounts_biotype_plot.txt:md5,6d251bec0231afccd0682e454a3b17bc",
                 "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49",
-                "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02",
                 "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e",
                 "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb",
@@ -1340,9 +1340,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:38:50.917761241"
+        "timestamp": "2025-01-28T13:45:28.520702162"
     }
-}
+}
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
@@ -273,10 +273,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:48:16.536464395"
+        "timestamp": "2025-01-28T13:49:54.341502957"
     },
     "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
         "content": [
@@ -360,9 +360,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:49:02.306667165"
+        "timestamp": "2025-01-28T13:50:34.753130451"
     }
-}
+}
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -264,10 +264,10 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt",
+                "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt",
                 "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt",
@@ -1077,11 +1077,11 @@
                 "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
-                "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476",
+                "multiqc_featurecounts_biotype_plot.txt:md5,7023aeba8868687d17107a265791f096",
                 "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
-                "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "qualimap_gene_coverage_profile_Counts.txt:md5,6d377444d29c3d4135980982ab1df2fb",
                 "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008",
                 "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee",
@@ -1195,10 +1195,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:57:05.836924025"
+        "timestamp": "2025-01-28T13:58:04.624400317"
     },
     "Params: --min_mapped_reads 90 - stub": {
         "content": [
@@ -1299,9 +1299,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-03T17:57:59.273391037"
+        "timestamp": "2025-01-28T13:58:55.550749008"
     }
-}
+}
diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap
@@ -424,6 +424,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-21T18:27:30.970398934"
+        "timestamp": "2025-01-28T14:01:08.126903467"
     }
 }