Revert "increase gatk logging level"

TCLamnidis · TCLamnidis · commit 1e4ab85e9dfd · 2026-01-21T22:53:20.000+01:00
This reverts commit 995a3b5.
diff --git a/conf/modules.config b/conf/modules.config
@@ -1646,7 +1646,6 @@ process {
                 "--output_mode ${params.genotyping_gatk_ug_out_mode}",
                 "--genotype_likelihoods_model ${params.genotyping_gatk_ug_genotype_mode}",
                 params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "",
-                "--logging_level DEBUG",
             ].join(' ').trim()
         }
         ext.prefix = { "${meta.sample_id}_${meta.reference}" }

Original file line number	Diff line number	Diff line change
`@@ -1646,7 +1646,6 @@ process {`
`1646`	`1646`	`"--output_mode ${params.genotyping_gatk_ug_out_mode}",`
`1647`	`1647`	`"--genotype_likelihoods_model ${params.genotyping_gatk_ug_genotype_mode}",`
`1648`	`1648`	`params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "",`
`1649`		`- "--logging_level DEBUG",`
`1650`	`1649`	`].join(' ').trim()`
`1651`	`1650`	`}`
`1652`	`1651`	`ext.prefix = { "${meta.sample_id}_${meta.reference}" }`