From 70071bf30da6cccfc701bca251b7a0f7a0a85b70 Mon Sep 17 00:00:00 2001 From: "joanna.krawczyk" Date: Tue, 23 Jul 2024 14:39:18 +0200 Subject: [PATCH 1/2] Fix No such variable: CUTADAPT error by replacing CUTADAPT.out with CUTADAPT_FIVE_PRIME and CUTADAPT_THREE_PRIME --- workflows/crisprseq_screening.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/crisprseq_screening.nf b/workflows/crisprseq_screening.nf index 5ccb9310..d2470b26 100644 --- a/workflows/crisprseq_screening.nf +++ b/workflows/crisprseq_screening.nf @@ -86,7 +86,7 @@ workflow CRISPRSEQ_SCREENING { [meta, fastq, proto] }.set { ch_cutadapt } - ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT.out.log.collect{it[1]}) + ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT_FIVE_PRIME.out.log.collect{it[1]}) ch_versions = ch_versions.mix(CUTADAPT_FIVE_PRIME.out.versions) } @@ -95,7 +95,7 @@ workflow CRISPRSEQ_SCREENING { ch_cutadapt ) ch_cutadapt = CUTADAPT_THREE_PRIME.out.reads.combine(Channel.value([[]])) - ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT.out.log.collect{it[1]}) + ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT_THREE_PRIME.out.log.collect{it[1]}) ch_versions = ch_versions.mix(CUTADAPT_THREE_PRIME.out.versions) } From 1da776911612704172d6e2cc1d1e28ea4d251fd1 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 25 Jul 2024 15:54:21 +0200 Subject: [PATCH 2/2] Add contributor in readme and change in changelog --- CHANGELOG.md | 2 ++ README.md | 1 + 2 files changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2112ed73..07d12cc4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- Fix cutadapt 3' and 5' no such variable found bug ([#187](https://github.com/nf-core/crisprseq/pull/187)) + ### Deprecated ## [v2.2.1 Romarin Curie - patch](https://github.com/nf-core/crisprseq/releases/tag/2.2.1) - [23.07.2024] diff --git a/README.md b/README.md index bbf08834..db4d217d 100644 --- a/README.md +++ b/README.md @@ -132,6 +132,7 @@ We thank the following people for their extensive assistance in the development - [@msanvicente](https://github.com/msanvicente) - [@mschaffer-incyte](https://github.com/mschaffer-incyte) - [@SusiJo](https://github.com/SusiJo) +- [@joannakraw](https://github.com/joannakraw) ## Contributions and Support