added the option to turn off the normalisation step

replikation · Jun 27, 2023 · 42f6604 · 42f6604
1 parent e4cf9dc
commit 42f6604
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diff --git a/poreCov.nf b/poreCov.nf
@@ -467,7 +467,8 @@ ${c_yellow}Inputs (choose one):${c_reset}
 
 ${c_yellow}Workflow control (optional)${c_reset}
     --artic_normalize        Normalise down to moderate coverage to save runtime [default: $params.artic_normalize]
-                                   ${c_dim}(after mapping and before variant calling in the ARTIC bioinformatics pipeline)${c_reset}
+                                   ${c_dim}(after mapping and before variant calling in the ARTIC bioinformatics pipeline)
+                                   Use `--artic_normalize False` to turn off this normalisation.${c_reset}
     --update                 Always try to use latest pangolin & nextclade release [default: $params.update]
     --samples                .csv input (header: Status,_id), renames barcodes (Status) by name (_id), e.g.:
                              Status,_id

diff --git a/workflows/process/artic.nf b/workflows/process/artic.nf
@@ -16,11 +16,12 @@ process artic_medaka {
         tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.*1.depths"), path("${name}.coverage_mask.txt.*2.depths"), emit: covarplot
         tuple val(name), path("${name}.trimmed.rg.sorted.bam"), emit: fullbam
     script:   
+        def normalise_arg = normalise_threshold ? "--normalise ${normalise_threshold}" : ''
         """
         artic minion    --medaka \
                         --medaka-model ${params.medaka_model} \
                         --min-depth ${params.min_depth} \
-                        --normalise ${normalise_threshold} \
+                        ${normalise_arg} \
                         --threads ${task.cpus} \
                         --scheme-directory ${external_scheme} \
                         --read-file ${reads} \