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Revert multiqc workaround #1359

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merged 4 commits into from
Aug 22, 2024
Merged

Revert multiqc workaround #1359

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4464227
Revert multiqc workaround due to fix
pinin4fjords Aug 21, 2024
9130eea
Update changelog
pinin4fjords Aug 21, 2024
27d8091
Update changelog
pinin4fjords Aug 21, 2024
52de9f6
Install properly
pinin4fjords Aug 22, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -114,6 +114,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width
- [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc
- [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests
- [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround

### Parameters

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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -92,7 +92,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "878d2adbb911aa6e15c06a4d1e93d01bd6f26c74",
"git_sha": "fb387b16025333f6d66b88d6c48c3719f47b1637",
"installed_by": ["modules"]
},
"picard/markduplicates": {
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2 changes: 1 addition & 1 deletion modules/nf-core/multiqc/environment.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/multiqc/main.nf
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6 changes: 3 additions & 3 deletions modules/nf-core/multiqc/tests/main.nf.test.snap
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6 changes: 4 additions & 2 deletions workflows/rnaseq/assets/multiqc/multiqc_config.yml
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Expand Up @@ -11,13 +11,13 @@ report_section_order:
fail_strand_check-module:
order: 5001
# Preprocessing and pre-alignment QC
fastqc:
fastqc_raw:
order: 4004
cutadapt:
order: 4003
fastp:
order: 4003
fastqc-1:
fastqc_trimmed:
order: 4002
# Alignment
star:
Expand Down Expand Up @@ -98,13 +98,15 @@ run_modules:

module_order:
- fastqc:
anchor: "fastqc_raw"
name: "FastQC (raw)"
info: "This section of the report shows FastQC results before adapter trimming."
path_filters:
- "*_raw*fastqc.zip"
- cutadapt
- fastp
- fastqc:
anchor: "fastqc_trimmed"
name: "FastQC (trimmed)"
info: "This section of the report shows FastQC results after adapter trimming."
path_filters:
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