uopdate args of medaka

genomic-medicine-sweden · Jan 10, 2025 · 0c4f16e · 0c4f16e
1 parent 0928c84
commit 0c4f16e
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -249,9 +249,10 @@ process {
         ]
     }
 
-    withName: '.*LONGREAD_CONSENSUS:MEDAKA_PARALLEL' {
+    withName: '.*LONGREAD_CONSENSUS:MEDAKA' {
         ext.prefix = { "${meta.id}_${meta.taxid}" }
-        //ext.args = '-g' // -g Don't fill gaps in consensus with draft sequence
+        ext.args1 = '-A'
+        ext.args3 = '--no-fillgaps' // Don't fill gaps in consensus with draft sequence
         publishDir = [
             path: { "$params.outdir/pathogens/consensus/" },
             mode: params.publish_dir_mode,

diff --git a/modules/local/medaka_consensus/main.nf b/modules/local/medaka_consensus/main.nf
@@ -33,7 +33,7 @@ process MEDAKA_PARALLEL {
     mini_align \\
         -i ${reads} \\
         -r \$assembly \\
-        -P -m \\
+        -m \\
         -t $task.cpus \\
         -p ${prefix}_calls_to_draft \\
         ${args1}