merged

bin/write_seqs.py

@@ -64,7 +64,8 @@ def main(arguments):
         formatter_class=argparse.RawDescriptionHelpFormatter)
     parser.add_argument(
         'seqtabs', nargs='*',
-        help='One or more headerless CSV files with columns specimen,count,seq')
+        help='One or more headerless CSV files '
+             'with columns specimen,count,seq')
     parser.add_argument(
         '--seqtablist', type=argparse.FileType('r'),
         help='A file listing one seqtab file per line')
@@ -91,6 +92,7 @@ def main(arguments):
     parser.add_argument(
         '--direction',
         choices=['merged', 'R1', 'R2'],
+        default='merged',
         help='label to add to all sequence names')
     parser.add_argument(
         '-j', '--num-processes', type=int, default=1,

main.nf

@@ -294,9 +294,9 @@ process dada_dereplicate {
         --counts counts.csv \
         --data dada.rds \
         --errors ${model} \
+        --nthreads ${params.nproc} \
         --orientation ${orientation} \
         --overlaps overlaps.csv \
-        --nthreads ${params.nproc} \
         --params ${dada_params} \
         --sampleid ${sampleid} \
         --seqtab seqtab.csv \

nextflow.config

@@ -93,6 +93,9 @@ profiles {
 
     uw_batch {
         workDir = 's3://molmicro-data/nextflow-workdir/dada2-nf'
+        params {
+            output = 'output'
+        }
         process {
             scratch = "/docker_scratch"
             queue = 'molmicro-queue'