Merge pull request #1308 from MatthiasZepper/MultiQC_FastQC_bug

Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling.
nf-core · Jul 12, 2024 · 18d8d10 · 18d8d10
2 parents 1af00b9 + 1c75669
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -82,6 +82,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1304](https://github.com/nf-core/rnaseq/pull/1304) - Remove redundant gene TPM outputs
 - [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison
 - [PR #1307](https://github.com/nf-core/rnaseq/pull/1307) - Clarify infer strandedness step in subway map and text
+- [PR #1308](https://github.com/nf-core/rnaseq/pull/1308) - Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling.
 - [PR #1309](https://github.com/nf-core/rnaseq/pull/1309) - Document FASTP sampling
 - [PR #1310](https://github.com/nf-core/rnaseq/pull/1310) - Reinstate pseudoalignment subworkflow config
 - [PR #1312](https://github.com/nf-core/rnaseq/pull/1312) - Fix issues with unzipping of GTF/ GFF files without absolute paths

diff --git a/docs/usage.md b/docs/usage.md
@@ -146,12 +146,13 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
 
 #### Examples:
 
-| UMI type     | Source                                                                                                                                                                                                                                               | Pipeline parameters                                                                                                                            |
-| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
-| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                      | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                   |
-| In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                          | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                   |
-| In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_       | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12` |
-| In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                  |
+| UMI type     | Source                                                                                                                                                                                                                                                                                                                              | Pipeline parameters                                                                                                                                                         |
+| ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                                                                                                     | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                                                |
+| In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                                                                                                         | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                                                |
+| In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_                                                                                      | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12`                              |
+| In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf)                                                                                | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                                               |
+| In sequence  | [Watchmaker mRNA Library Prep Kit](https://watchmakergenomics.com/wp-content/uploads/2023/11/M223_mRNA-Library-Prep-Kit-_UG_WMUG214_v1-1-0823.pdf) with [Twist UMI Adapter System](https://www.twistbioscience.com/sites/default/files/resources/2023-03/DOC-001337_TechNote-ProcessingSequencingDataUtilizingUMI-REV1-singles.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{5})(?P<discard_1>.{2}).*" --umitools_bc_pattern2 "^(?P<umi_2>.{5})(?P<discard_2>.{2}).*"` |
 
 > _No warranty for the accuracy or completeness of the parameters is implied_
 

diff --git a/modules.json b/modules.json
@@ -37,9 +37,8 @@
                     },
                     "dupradar": {
                         "branch": "master",
-                        "git_sha": "f632a6e25b05497477920183cff33ba72ab7b6fc",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/dupradar/dupradar.diff"
+                        "git_sha": "055416736dcb4955960ecc17dea61eb41b68c024",
+                        "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
@@ -93,7 +92,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "314d742bdb357a1df5f9b88427b3b6ac78aa33f7",
+                        "git_sha": "45d482f013f7da8a3e050e855f04ada418d91c3c",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {

diff --git a/modules/nf-core/dupradar/dupradar.diff b/modules/nf-core/dupradar/dupradar.diff
diff --git a/modules/nf-core/dupradar/main.nf b/modules/nf-core/dupradar/main.nf
diff --git a/modules/nf-core/dupradar/templates/dupradar.r b/modules/nf-core/dupradar/templates/dupradar.r