Fixed trim galore process

NCBI-Hackathons · Jun 23, 2018 · 4cf7a90 · 4cf7a90
1 parent 4913b17
commit 4cf7a90
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -17,7 +17,7 @@ params {
   genome = "$baseDir/test-data/genome/genome.fa"
   bt2index = "$baseDir/test-data/bowtie2-index/genome"
   chrom_sizes = "$baseDir/test-data/genome-data/sizes.genome"
-  tf_motif_sites = "/tmp"
+  tf_motif_sites = "$baseDir/test-data/motifs/human_hg19"
   readPaths = [
     ['SRR5204807', ["$baseDir/test-data/reads/SRR5204807_1.fastq.gz", "$baseDir/test-data/reads/SRR5204807_2.fastq.gz"]],
     ['SRR5204808', ["$baseDir/test-data/reads/SRR5204808_1.fastq.gz", "$baseDir/test-data/reads/SRR5204808_2.fastq.gz"]]

diff --git a/main.nf b/main.nf
@@ -237,7 +237,7 @@ process trim_galore {
     set val(name), file(reads) from read_files_trimming
 
     output:
-    set val(name), file("*.gz") into trimmed_reads_ch
+    set val(name), file("*.fq.gz") into trimmed_reads_ch
     file "*trimming_report.txt" into trimgalore_results
 
     script:
@@ -247,7 +247,7 @@ process trim_galore {
         """
     } else {
         """
-        trim_galore --fastqc --gzip $reads
+        trim_galore --paired --gzip $reads
         """
     }
 }