From 41fd8c9a023f360383f178c09ad54619a2ff9680 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 5 Sep 2024 16:36:55 +0200 Subject: [PATCH 1/4] fix saving merged fastq files in fastp module --- conf/modules.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 35248e4..0304051 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -270,6 +270,12 @@ if (!params.skip_fastp) { mode: params.publish_dir_mode, pattern: "*.fail.fastq.gz", enabled: params.save_trimmed_fail + ], + [ + path: { "${params.outdir}/trimming/shortreads" }, + mode: params.publish_dir_mode, + pattern: "*.merged.fastq.gz", + enabled: params.save_merged ] ] } From 7f438ecda52aa6838e9c5692930a9111f3499ddd Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 5 Sep 2024 17:17:43 +0200 Subject: [PATCH 2/4] #163 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4ae6d43..5e2ef25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues. From f1f915cb2fc3cc48a8f060d02a9f5ffdf99d8f40 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 6 Sep 2024 13:58:02 +0200 Subject: [PATCH 3/4] extend description on save_merged param --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5c40fdd..a058d28 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -56,7 +56,7 @@ }, "save_merged": { "type": "boolean", - "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`" + "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`. This option enables read merging and saves all merged reads to a file ending in `*.merged.fastq.gz`; these reads will be won't be passed to the assembly process." }, "skip_fastqc": { "type": "boolean", From 6e0d781e8ff61135b70d9f674d1ec06c8e103797 Mon Sep 17 00:00:00 2001 From: Daniel VM <69470278+Daniel-VM@users.noreply.github.com> Date: Fri, 6 Sep 2024 14:02:20 +0200 Subject: [PATCH 4/4] Fix CHANGELOG.md #163 Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e2ef25..ad1c58c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files +- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files. - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues.