Fix HC caller command as they renamed the parameter

jfy133 · jfy133 · commit f48cfebb2ca9 · 2025-04-04T09:26:09.000Z
diff --git a/conf/modules.config b/conf/modules.config
@@ -1648,7 +1648,7 @@ process {
         tag        = { "${meta.reference}|${meta.sample_id}" }
         ext.args   = {
             [
-                meta2.ploidy ? "--sample_ploidy ${meta2.ploidy}" : "--sample_ploidy 2",
+                meta2.ploidy ? "--sample-ploidy ${meta2.ploidy}" : "--sample-ploidy 2",
                 "-stand-call-conf ${params.genotyping_gatk_call_conf}",
                 "--output-mode ${params.genotyping_gatk_hc_out_mode}",
                 "--emit-ref-confidence ${params.genotyping_gatk_hc_emitrefconf}",

Original file line number	Diff line number	Diff line change
`@@ -1648,7 +1648,7 @@ process {`
`1648`	`1648`	`tag = { "${meta.reference}\|${meta.sample_id}" }`
`1649`	`1649`	`ext.args = {`
`1650`	`1650`	`[`
`1651`		`- meta2.ploidy ? "--sample_ploidy ${meta2.ploidy}" : "--sample_ploidy 2",`
	`1651`	`+ meta2.ploidy ? "--sample-ploidy ${meta2.ploidy}" : "--sample-ploidy 2",`
`1652`	`1652`	`"-stand-call-conf ${params.genotyping_gatk_call_conf}",`
`1653`	`1653`	`"--output-mode ${params.genotyping_gatk_hc_out_mode}",`
`1654`	`1654`	`"--emit-ref-confidence ${params.genotyping_gatk_hc_emitrefconf}",`