From 2d9bdbb6174fdc6ee36afebb3e15e72afaa5ea33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pontus=20H=C3=B6jer?= Date: Mon, 13 Oct 2025 15:51:57 +0200 Subject: [PATCH 1/4] fix broken link and add latest kit version --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 00cac88b2..6e6621f80 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -252,7 +252,7 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic | 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.{6})(?P.{4}).*"` | | In sequence | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)
> _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.{12}).*"`
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.{8})(?P.{6}).*"` | +| In sequence | Takara Bio [SMART-Seq Total RNA Pico Input with UMIs](https://www.takarabio.com/documents/User%20Manual/SMART/SMART-Seq%20Total%20RNA%20Pico%20Input%20with%20UMIs%20%28ZapR%20Mammalian%29%20User%20Manual.pdf) and [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_114950.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P.{8})(?P.{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.{5})(?P.{2}).*" --umitools_bc_pattern2 "^(?P.{5})(?P.{2}).*"` | > _No warranty for the accuracy or completeness of the parameters is implied_ From d43c00d31c9009f6c04030f4860c9ee805945d37 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pontus=20H=C3=B6jer?= Date: Mon, 13 Oct 2025 14:02:43 +0000 Subject: [PATCH 2/4] run prettier --- docs/usage.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 6e6621f80..296f87da5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -247,13 +247,13 @@ 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.{6})(?P.{4}).*"` | -| In sequence | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)
> _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.{12}).*"`
Optional: `--clip_r2 9 --three_prime_clip_r2 12` | -| In sequence | Takara Bio [SMART-Seq Total RNA Pico Input with UMIs](https://www.takarabio.com/documents/User%20Manual/SMART/SMART-Seq%20Total%20RNA%20Pico%20Input%20with%20UMIs%20%28ZapR%20Mammalian%29%20User%20Manual.pdf) and [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_114950.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P.{8})(?P.{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.{5})(?P.{2}).*" --umitools_bc_pattern2 "^(?P.{5})(?P.{2}).*"` | +| 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.{6})(?P.{4}).*"` | +| In sequence | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)
> _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.{12}).*"`
Optional: `--clip_r2 9 --three_prime_clip_r2 12` | +| In sequence | Takara Bio [SMART-Seq Total RNA Pico Input with UMIs](https://www.takarabio.com/documents/User%20Manual/SMART/SMART-Seq%20Total%20RNA%20Pico%20Input%20with%20UMIs%20%28ZapR%20Mammalian%29%20User%20Manual.pdf) and [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_114950.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P.{8})(?P.{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.{5})(?P.{2}).*" --umitools_bc_pattern2 "^(?P.{5})(?P.{2}).*"` | > _No warranty for the accuracy or completeness of the parameters is implied_ From 45bded1cca37c582d485adb0df08eb9e3c265d6f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 13 Nov 2025 12:33:48 +0000 Subject: [PATCH 3/4] Update CHANGELOG.md for PRs #1613 and #1614 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Add entry for PR #1613: Fix broken link and add latest kit version for Takara UMI prep - Add entry for PR #1614: Template update for nf-core/tools v3.4.1 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d42fcdde3..8060deb1e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements and fixes - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0 +- [PR #1613](https://github.com/nf-core/rnaseq/pull/1613) - Fix broken link and add latest kit version for Takara UMI prep in usage documentation +- [PR #1614](https://github.com/nf-core/rnaseq/pull/1614) - Template update for nf-core/tools v3.4.1 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18 From 81a6ae9c2e4e65179de5c69493544bf32cd7dee6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 13 Nov 2025 12:38:54 +0000 Subject: [PATCH 4/4] =?UTF-8?q?Add=20Pontus=20H=C3=B6jer=20to=20Credits=20?= =?UTF-8?q?for=20next=20release?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8060deb1e..9cd94e2b4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Credits +Special thanks to the following for their contributions to the release: + +- [Pontus Höjer](https://github.com/pontushojer) + ### Enhancements and fixes - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0