Merge pull request nf-core#393 from BU-ISCIII/artic_primers

Changed primer set to params
BU-ISCIII · Jan 16, 2024 · ce72f48 · ce72f48
2 parents be0473b + d6ff06c
commit ce72f48
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diff --git 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
 

diff --git a/README.md b/README.md
@@ -138,6 +138,7 @@ nextflow run nf-core/viralrecon \
    --outdir <OUTDIR> \
    --platform nanopore \
    --genome 'MN908947.3' \
+   --primer_set 'artic' \
    --primer_set_version 3 \
    --fastq_dir fastq_pass/ \
    --fast5_dir fast5_pass/ \

diff --git 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
@@ -28,6 +28,7 @@ params {
 
     // Genome references
     genome             = 'MN908947.3'
+    primer_set         = 'artic'
     primer_set_version = 3
 
     // variant calling options

diff --git a/docs/usage.md b/docs/usage.md
@@ -104,6 +104,7 @@ nextflow run nf-core/viralrecon \
     --outdir <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 <OUTDIR> \
     --platform nanopore \
     --genome 'MN908947.3' \
+    --primer_set 'artic' \
     --primer_set_version 3 \
     --fastq_dir fastq_pass/ \
     --artic_minion_caller medaka \

diff --git 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)
 }