From 73bb74dff62acc23ad017d8d1fb16eb04f598a18 Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Thu, 27 May 2021 09:47:28 +0200 Subject: [PATCH 1/5] Renamed param --mean_quality to --fastp_qualified_quality and adjusted description --- conf/modules.config | 4 ++-- nextflow.config | 2 +- nextflow_schema.json | 5 +++-- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4ceb47695..e7c817a70 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -23,8 +23,8 @@ params { publish_files = ['html':''] publish_dir = "QC_shortreads/fastqc" } - 'fastp' { // TODO check parameter: -q vs -e? - args = "-q ${params.mean_quality} --cut_by_quality5 --cut_by_quality3 --cut_mean_quality ${params.trimming_quality}" + 'fastp' { + args = "-q ${params.fastp_qualified_quality} --cut_by_quality5 --cut_by_quality3 --cut_mean_quality ${params.trimming_quality}" publish_files = ['html':'', 'json':''] publish_by_id = true publish_dir = "QC_shortreads/fastp" diff --git a/nextflow.config b/nextflow.config index 0daa0c79c..fe1b478e5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { // short read preprocessing options save_trimmed_fail = false - mean_quality = 15 + fastp_qualified_quality = 15 trimming_quality = 15 keep_phix = false // phix_reference = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz" diff --git a/nextflow_schema.json b/nextflow_schema.json index 9526c2634..08d9846a6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -303,10 +303,11 @@ "description": "Save the trimmed FastQ files in the results directory.", "help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete." }, - "mean_quality": { + "fastp_qualified_quality": { "type": "integer", "default": 15, - "description": "Mean qualified quality value for keeping read." + "description": "Minimum phred quality value of a base to be qualified.", + "help": "Reads with more than 40% of unqualified bases will be discarded." }, "trimming_quality": { "type": "integer", From e0f17e54a01eabb97a41e2fab0d62a34144eb360 Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Thu, 27 May 2021 10:23:23 +0200 Subject: [PATCH 2/5] Renamed param --trimming_quality to --fastp_cut_mean_quality and adjusted description --- conf/modules.config | 2 +- nextflow.config | 2 +- nextflow_schema.json | 5 +++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e7c817a70..b041fa7b2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -24,7 +24,7 @@ params { publish_dir = "QC_shortreads/fastqc" } 'fastp' { - args = "-q ${params.fastp_qualified_quality} --cut_by_quality5 --cut_by_quality3 --cut_mean_quality ${params.trimming_quality}" + args = "-q ${params.fastp_qualified_quality} --cut_by_quality5 --cut_by_quality3 --cut_mean_quality ${params.fastp_cut_mean_quality}" publish_files = ['html':'', 'json':''] publish_by_id = true publish_dir = "QC_shortreads/fastp" diff --git a/nextflow.config b/nextflow.config index fe1b478e5..725bd0ef4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -15,7 +15,7 @@ params { // short read preprocessing options save_trimmed_fail = false fastp_qualified_quality = 15 - trimming_quality = 15 + fastp_cut_mean_quality = 15 keep_phix = false // phix_reference = "ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Enterobacteria_phage_phiX174_sensu_lato/all_assembly_versions/GCA_002596845.1_ASM259684v1/GCA_002596845.1_ASM259684v1_genomic.fna.gz" phix_reference = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz" diff --git a/nextflow_schema.json b/nextflow_schema.json index 08d9846a6..bc754617a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -309,10 +309,11 @@ "description": "Minimum phred quality value of a base to be qualified.", "help": "Reads with more than 40% of unqualified bases will be discarded." }, - "trimming_quality": { + "fastp_cut_mean_quality": { "type": "integer", "default": 15, - "description": "Trimming quality value for the sliding window." + "description": "The mean quality requirement used for per read sliding window cutting by fastp.", + "help": "Used in combination with the fastp options '--cut_front' and '--cut_tail'. If the mean quality within a window (of size 4) is below `--fastp_cut_mean_quality`, the bases are dropped and the sliding window is moved further, otherwise it stops." }, "host_genome": { "type": "string", From 8d94692e0b3145df39cc2bd71b6a97b52482e376 Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Thu, 27 May 2021 10:25:42 +0200 Subject: [PATCH 3/5] Replaced deprecated fastp params --cut_by_quality5/3 by --cut_front/tail --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index b041fa7b2..15445f06a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -24,7 +24,7 @@ params { publish_dir = "QC_shortreads/fastqc" } 'fastp' { - args = "-q ${params.fastp_qualified_quality} --cut_by_quality5 --cut_by_quality3 --cut_mean_quality ${params.fastp_cut_mean_quality}" + args = "-q ${params.fastp_qualified_quality} --cut_front --cut_tail --cut_mean_quality ${params.fastp_cut_mean_quality}" publish_files = ['html':'', 'json':''] publish_by_id = true publish_dir = "QC_shortreads/fastp" From 2b51c46ae46d475aff5685cec10b40d5d1c31cf4 Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Thu, 27 May 2021 10:29:46 +0200 Subject: [PATCH 4/5] Adjust desscription of fast param --save_trimmed_fail --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index bc754617a..2b4a5a2dd 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -300,7 +300,7 @@ "save_trimmed_fail": { "type": "boolean", "fa_icon": "fas fa-save", - "description": "Save the trimmed FastQ files in the results directory.", + "description": "Save the by fastp trimmed FastQ files in the results directory.", "help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete." }, "fastp_qualified_quality": { From 255653b62dbfc63e84cfce40cf403dfb975663f2 Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Thu, 27 May 2021 10:37:57 +0200 Subject: [PATCH 5/5] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b6d69d68b..39a639204 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#193](https://github.com/nf-core/mag/pull/193) - Compress CAT output files [#180](https://github.com/nf-core/mag/issues/180) - [#198](https://github.com/nf-core/mag/pull/198) - Requires nextflow version `>= 21.04.0` - [#200](https://github.com/nf-core/mag/pull/200) - Small changes in GitHub Actions tests +- [#203](https://github.com/nf-core/mag/pull/203) - Renamed `fastp` params and improved description in documentation: `--mean_quality` -> `--fastp_qualified_quality`, `--trimming_quality` -> `--fastp_cut_mean_quality` ### `Fixed`