Merge pull request #145 from Joon-Klaps/small-patch

modifying the ivar_consensus params

conf/modules.config

@@ -924,7 +924,8 @@ process {
             withName: IVAR_CONTIG_CONSENSUS {
                 ext.prefix = { "${meta.id}_consensus" } // DON'T CHANGE
                 ext.args = [
-                    '-t 0.51',  // frequency to call consensus: 0.51 just the majority rule
+                    '-t 0',     // minmum frequency threshhold, majority rule
+                    '-c 0.1',   // minimum insertion frequency threshold: 10% needs to have the insert in order for it to be considered
                     '-q 0',     // minimum quality score : 0 (no quality is provided)
                     '-m 1',     // minimum depth to call consensus
                     '-n N'      // Characters to print in regions with less coverage
@@ -1511,12 +1512,16 @@ process {
         }
 
         withName: IVAR_CONSENSUS {
-            ext.args = [
-                '-t 0.75',          // frequency to call consensus: 0.75 just the majority rule
-                '-q 20',            // minimum quality score of base
-                '-m 10',            // minimum depth to call consensus
-                '-n N'              // Characters to print in regions with less coverage
-            ].join(' ').trim()
+            ext.args = {
+                def baseArgs = [
+                    '-t 0',          // frequency to call consensus, majority rule
+                    '-q 20',         // minimum quality score of base
+                    '-m 10',         // minimum depth to call consensus
+                    '-n N',          // Characters to print in regions with less coverage
+                ].join(' ').trim()
+                def cValue = (meta.iteration as String).isInteger() ? "-c ${0.41 + (meta.iteration as int) * 0.10}": ''
+                return "${baseArgs} ${cValue}"
+            }
             ext.args2 = [
                 '--count-orphans',  // Do not skip anomalous read pairs in variant calling.
                 '--max-depth 0',    // Maximum number of reads to start to consider at each location, 0 means no limit