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conf/modules/bwameth_align.config

@@ -1,12 +1,5 @@
 process {
     withName: BWAMETH_ALIGN {
         cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
-        ext.args = ''
-        publishDir = [
-                path: { "${params.outdir}/${params.aligner}/alignments" },
-                pattern: "*.bam",
-                mode: params.publish_dir_mode,
-                enabled: params.save_align_intermeds
-        ]
     }
 }

conf/modules/parabricks_fq2bammeth.config

@@ -1,12 +1,5 @@
 process {
     withName: PARABRICKS_FQ2BAMMETH {
         cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
-        ext.args = '--low-memory'
-        publishDir = [
-                path: { "${params.outdir}/${params.aligner}/alignments" },
-                pattern: "*.bam",
-                mode: params.publish_dir_mode,
-                enabled: params.save_align_intermeds
-        ]
     }
 }