added primary

otb.sh

@@ -17,7 +17,7 @@ help(){
        display otb version and exit
 
     -s or --supress
-       supress stop and checks, and submit without sending to background
+       supress \"stop and gather user input\", and submit without sending to background
 
     -c or --check
        perform checks to insure smoother operation
@@ -35,7 +35,7 @@ help(){
 
   suggested:
     -m or --mode
-       mode to use, must be one of \"phasing\",\"homozygous\",\"heterozygous\",\"trio\", default: homozygous
+       mode to use, must be one of \"phasing\",\"homozygous\",\"heterozygous\",\"primary\",\"trio\", default: homozygous
 
     -t or --threads
        number of threads to use, clusters sometimes use this as number of cores, default: 20

run.nf

@@ -207,6 +207,14 @@ process HiFiASM {
     sleep 120;
     exit 0;
   """
+  else if( params.mode == 'primary')
+  """
+    touch hifiasm.flag.txt
+    hifiasm -o ${params.assembly} --primary -t ${task.cpus} --write-paf --write-ec ${fasta} 2>&1
+    echo "finished alignment"
+    sleep 120;
+    exit 0;
+  """
   else if ( params.mode == 'trio')
   """
     touch hifiasm.flag.txt