From b96fc774f1994a58bab302d1aa85350a647bd116 Mon Sep 17 00:00:00 2001 From: svarona Date: Fri, 18 Aug 2023 12:38:33 +0200 Subject: [PATCH 1/6] Changed primer set to params --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index e51c832d..fd4468ef 100644 --- a/main.nf +++ b/main.nf @@ -23,7 +23,7 @@ if (params.platform == 'illumina' && params.protocol == 'amplicon') { primer_set = params.primer_set primer_set_version = params.primer_set_version } else if (params.platform == 'nanopore') { - primer_set = 'artic' + primer_set = params.primer_set primer_set_version = params.primer_set_version params.artic_scheme = WorkflowMain.getGenomeAttribute(params, 'scheme', log, primer_set, primer_set_version) } From 79a67f0b4db1c6d9ead9e3667c1df2b5c46ef9bf Mon Sep 17 00:00:00 2001 From: svarona Date: Wed, 23 Aug 2023 13:44:26 +0200 Subject: [PATCH 2/6] Added artic to nextflow config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 812a2dfd..78489bd2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,7 @@ params { // Reference genome options genome = null - primer_set = null + primer_set = 'artic' primer_set_version = null primer_fasta = null primer_left_suffix = '_LEFT' From 06e82cf057fbcc079f237130467326dd59edf838 Mon Sep 17 00:00:00 2001 From: svarona Date: Wed, 23 Aug 2023 13:51:10 +0200 Subject: [PATCH 3/6] Moved artic primer params value from nextflow config to nanopore test config --- conf/test_full_nanopore.config | 1 + conf/test_nanopore.config | 1 + nextflow.config | 2 +- 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/conf/test_full_nanopore.config b/conf/test_full_nanopore.config index ec041051..43fceae1 100644 --- a/conf/test_full_nanopore.config +++ b/conf/test_full_nanopore.config @@ -23,6 +23,7 @@ params { // Genome references genome = 'MN908947.3' + primer_set = 'artic' primer_set_version = 3 // variant calling options diff --git a/conf/test_nanopore.config b/conf/test_nanopore.config index 0674e8ab..dfcc65c9 100644 --- a/conf/test_nanopore.config +++ b/conf/test_nanopore.config @@ -28,6 +28,7 @@ params { // Genome references genome = 'MN908947.3' + primer_set = 'artic' primer_set_version = 3 // variant calling options diff --git a/nextflow.config b/nextflow.config index 78489bd2..812a2dfd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,7 @@ params { // Reference genome options genome = null - primer_set = 'artic' + primer_set = null primer_set_version = null primer_fasta = null primer_left_suffix = '_LEFT' From addd692cd726bcd739b0551722b60da108913677 Mon Sep 17 00:00:00 2001 From: svarona Date: Mon, 23 Oct 2023 13:00:00 +0200 Subject: [PATCH 4/6] Added PR to CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 52ae7f0e..0f0676a3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [[#299](https://github.com/nf-core/viralrecon/issues/299)] - Add the freyja pipeline as a subworkflow - [[PR #387](https://github.com/nf-core/viralrecon/pull/387)] - Software closes gracefully when encountering an error - [[PR #395](https://github.com/nf-core/viralrecon/pull/395)] - Remove minia from default assemblers because it is unreliable +- [[PR #393](https://github.com/nf-core/viralrecon/pull/393)] - Changed primer set to params ### Parameters From 7b19b0a1cb1d3f0f8df59ff0802359ddaf7a7389 Mon Sep 17 00:00:00 2001 From: svarona Date: Tue, 16 Jan 2024 15:06:21 +0100 Subject: [PATCH 5/6] added primer set artic to usage example --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 3eac4923..46fbea6a 100644 --- a/README.md +++ b/README.md @@ -138,6 +138,7 @@ nextflow run nf-core/viralrecon \ --outdir \ --platform nanopore \ --genome 'MN908947.3' \ + --primer_set 'artic' \ --primer_set_version 3 \ --fastq_dir fastq_pass/ \ --fast5_dir fast5_pass/ \ From d6ff06cd8e43b69897cd91225464bf62c3655132 Mon Sep 17 00:00:00 2001 From: svarona Date: Tue, 16 Jan 2024 15:07:49 +0100 Subject: [PATCH 6/6] added primerset artic to usage examples --- docs/usage.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 93c0c4b0..c5aacc24 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -104,6 +104,7 @@ nextflow run nf-core/viralrecon \ --outdir \ --platform nanopore \ --genome 'MN908947.3' \ + --primer_set 'artic' \ --primer_set_version 3 \ --fastq_dir fastq_pass/ \ --fast5_dir fast5_pass/ \ @@ -123,6 +124,7 @@ nextflow run nf-core/viralrecon \ --outdir \ --platform nanopore \ --genome 'MN908947.3' \ + --primer_set 'artic' \ --primer_set_version 3 \ --fastq_dir fastq_pass/ \ --artic_minion_caller medaka \