Prettier on Markdown documents.

Author: MatthiasZepper

CHANGELOG.md

@@ -10,7 +10,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#1125](https://github.com/nf-core/rnaseq/issues/1125)][[#1126](https://github.com/nf-core/rnaseq/pull/1126)] - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`.
 - [[#1127](https://github.com/nf-core/rnaseq/pull/)] - Enlarge sampling to determine the number of columns in `filter_gtf.py` script.
 
-
 ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17
 
 ### Enhancements and fixes

docs/usage.md

@@ -93,9 +93,9 @@ 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 ":"`                                                                                   |
+| 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}).*"`                                  |