Skip to content

Bump MultiQC module to 1.27 #1499

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
pinin4fjords merged 5 commits into from
Jan 30, 2025
Merged

Bump MultiQC module to 1.27 #1499

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
e7d0f31
Bump multiqc module
pinin4fjords Jan 29, 2025
20d86cb
Update CHANGELOG
pinin4fjords Jan 29, 2025
51db118
Re-remove tags
pinin4fjords Jan 29, 2025
613fb9e
Re-remove tags
pinin4fjords Jan 29, 2025
4a355a7
update snaps
pinin4fjords Jan 28, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
2 changes: 1 addition & 1 deletion modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
"installed_by": ["modules"]
},
"picard/markduplicates": {
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/multiqc/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions modules/nf-core/multiqc/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

5 changes: 4 additions & 1 deletion modules/nf-core/multiqc/nextflow.config
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

24 changes: 12 additions & 12 deletions modules/nf-core/multiqc/tests/main.nf.test.snap
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

28 changes: 14 additions & 14 deletions tests/default.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
}
26 changes: 13 additions & 13 deletions tests/featurecounts_group_type.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
}
28 changes: 14 additions & 14 deletions tests/hisat2.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
}
14 changes: 7 additions & 7 deletions tests/kallisto.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand Down Expand Up @@ -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"
}
}
}
28 changes: 14 additions & 14 deletions tests/min_mapped_reads.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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"
}
}
}
2 changes: 1 addition & 1 deletion tests/nofasta.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"
}
}
Loading