From 3824d680df35cb4e5d8444b4a8c304ce3a871456 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Thu, 4 Apr 2024 08:19:50 +0000 Subject: [PATCH 1/2] accept auto-detect as parameter value to activate adapter auto detection --- CHANGELOG.md | 1 + conf/modules.config | 12 ++++++------ docs/usage.md | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d8f261b..7e547293 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [input channel cardinality](https://github.com/nf-core/smrnaseq/issues/331) in `MIRDEEP2_RUN` module - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [bowtie conda version](https://github.com/nf-core/smrnaseq/issues/333) in `BOWTIE_MAP_SEQ` module - [[#335]](https://github.com/nf-core/smrnaseq/pull/335) - Final fix for [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module +- [[#337]](https://github.com/nf-core/smrnaseq/pull/337) - Fix [three_prime_adapter issue](https://github.com/nf-core/smrnaseq/issues/327), allow `auto-detect` as value ### Software dependencies diff --git a/conf/modules.config b/conf/modules.config index f7a50622..4130afa7 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -47,12 +47,12 @@ process { // withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' { ext.args = [ "", - params.trim_fastq ? "" : "--disable_adapter_trimming", - params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1. - params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed. - params.fastp_min_length > 0 ? "-l ${params.fastp_min_length}" : "", - params.fastp_max_length > 0 ? "--max_len1 ${params.fastp_max_length}" : "", - params.three_prime_adapter == null ? '' : "--adapter_sequence ${params.three_prime_adapter}" + params.trim_fastq ? "" : "--disable_adapter_trimming", + params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1. + params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed. + params.fastp_min_length > 0 ? "-l ${params.fastp_min_length}" : "", + params.fastp_max_length > 0 ? "--max_len1 ${params.fastp_max_length}" : "", + params.three_prime_adapter == "auto-detect" ? "" : "--adapter_sequence ${params.three_prime_adapter}" ].join(" ").trim() publishDir = [ [ diff --git a/docs/usage.md b/docs/usage.md index b5eb01f0..881bb2ff 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -18,7 +18,7 @@ This option indicates the experimental protocol used for the sample preparation. The parameter `--three_prime_adapter` is set to the Illumina TruSeq single index adapter sequence `AGATCGGAAGAGCACACGTCTGAACTCCAGTCA`. This is also to ensure, that the auto-detect functionality of `FASTP` is disabled. Please make sure to adapt this adapter sequence accordingly for your run. -:warning: At least the `custom` protocol has to be specified, otherwise the pipeline won't run. In case you specify the `custom` protocol, ensure that the parameters above are set accordingly or the defaults will be applied. If you want to auto-detect the adapters using `fastp`, please set `--three_prime_adapter` to `""`. +:warning: At least the `custom` protocol has to be specified, otherwise the pipeline won't run. In case you specify the `custom` protocol, ensure that the parameters above are set accordingly or the defaults will be applied. If you want to auto-detect the adapters using `fastp`, please set `--three_prime_adapter` to `auto-detect`. ### `mirtrace_species` or `mirgenedb_species` From 2bfbbd5a6936abc8c5ebfe22341f71b78f0a5460 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Thu, 4 Apr 2024 08:22:04 +0000 Subject: [PATCH 2/2] reference correct issue in CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e547293..872a049d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [input channel cardinality](https://github.com/nf-core/smrnaseq/issues/331) in `MIRDEEP2_RUN` module - [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [bowtie conda version](https://github.com/nf-core/smrnaseq/issues/333) in `BOWTIE_MAP_SEQ` module - [[#335]](https://github.com/nf-core/smrnaseq/pull/335) - Final fix for [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module -- [[#337]](https://github.com/nf-core/smrnaseq/pull/337) - Fix [three_prime_adapter issue](https://github.com/nf-core/smrnaseq/issues/327), allow `auto-detect` as value +- [[#337]](https://github.com/nf-core/smrnaseq/pull/337) - Fix [three_prime_adapter issue](https://github.com/nf-core/smrnaseq/issues/326), allow `auto-detect` as value ### Software dependencies