added parameter to pipeline

loosolab · Dec 3, 2018 · a5259fd · a5259fd
1 parent 476df0c
commit a5259fd
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/pipeline.nf b/pipeline.nf
@@ -116,7 +116,7 @@ process glam2 {
 
     script:
     """
-    glam2 n ${fasta} -O . -a 10 -b 20 -z 5
+    glam2 n ${fasta} -O . -a ${params.motif_min_len} -b ${params.motif_max_len} -z 5
     """
 }
 
@@ -138,7 +138,7 @@ process tomtom {
 
     script:
     """
-    tomtom ${meme} ${jaspar_db} -thresh 0.01 -text --norc | sed '/^#/ d' | sed '/^\$/d' > ${name}_known_motif.tsv
+    tomtom ${meme} ${jaspar_db} -thresh ${params.tomtom_treshold} -text --norc | sed '/^#/ d' | sed '/^\$/d' > ${name}_known_motif.tsv
     """
 }