Make using sample ID as locustag optional

BCCDC-PHL · May 17, 2024 · 94d68c0 · 94d68c0
1 parent c8b63aa
commit 94d68c0
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Showing 3 changed files with 12 additions and 2 deletions.
diff --git a/modules/bakta.nf b/modules/bakta.nf
@@ -17,6 +17,7 @@ process bakta {
     tuple val(sample_id), path("${sample_id}_${assembler}_${assembly_mode}_bakta_provenance.yml"), emit: provenance
 
     script:
+    locustag = params.use_sample_id_as_locus_tag ? "--locust-tag \"${sample_id}\"" : ""
     """
     printf -- "- process_name: bakta\\n"                                     >> ${sample_id}_${assembler}_${assembly_mode}_bakta_provenance.yml
     printf -- "  tools:\\n"                                                  >> ${sample_id}_${assembler}_${assembly_mode}_bakta_provenance.yml
@@ -39,7 +40,7 @@ process bakta {
         --db ${params.bakta_db} \
         --compliant \
         --keep-contig-headers \
-        --locus-tag ${sample_id} \
+        ${locustag} \
         --prefix "${sample_id}" \
         ${assembly}
 

diff --git a/modules/prokka.nf b/modules/prokka.nf
@@ -15,6 +15,7 @@ process prokka {
     tuple val(sample_id), path("${sample_id}_${assembler}_${assembly_mode}_prokka_provenance.yml"), emit: provenance
 
     script:
+    locustag = params.use_sample_id_as_annotation_locustag ? "--locustag \"${sample_id}\"" : ""
     """
     printf -- "- process_name: prokka\\n"                                          >> ${sample_id}_${assembler}_${assembly_mode}_prokka_provenance.yml
     printf -- "  tools:\\n"                                                        >> ${sample_id}_${assembler}_${assembly_mode}_prokka_provenance.yml
@@ -24,7 +25,13 @@ process prokka {
     printf -- "        - parameter: --compliant\\n"                                >> ${sample_id}_${assembler}_${assembly_mode}_prokka_provenance.yml
     printf -- "          value: null\\n"                                           >> ${sample_id}_${assembler}_${assembly_mode}_prokka_provenance.yml
 
-    prokka --cpus ${task.cpus} --compliant --locustag ${sample_id} --centre "BCCDC-PHL" --prefix "${sample_id}" ${assembly}
+    prokka \
+	--cpus ${task.cpus} \
+	--compliant \
+	${locustag} \
+	--centre "${params.annotation_centre}" \
+	--prefix "${sample_id}" \
+	${assembly}
 
     cp ${sample_id}/${sample_id}.gbk ${sample_id}_${assembler}_${assembly_mode}_prokka.gbk
     cp ${sample_id}/${sample_id}.gff ${sample_id}_${assembler}_${assembly_mode}_prokka.gff

diff --git a/nextflow.config b/nextflow.config
@@ -23,6 +23,8 @@ params {
     filtlong_min_length = 1000
     filtlong_keep_percent = 90
     samplesheet_input = 'NO_FILE'
+    use_sample_id_as_annotation_locustag = false
+    annotation_centre = 'BCCDC-PHL'
     pipeline_short_name = parsePipelineName(manifest.toMap().get('name'))
     pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version'))
 }