Fix outdir for fastqc ci and process

.gitlab-ci.yml

@@ -70,7 +70,7 @@ dedupData:
 fastqc:
   stage: unit
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz .
+  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz -o .
   - pytest -m fastqc
 
 integration_se:

workflow/rna-seq.nf

@@ -354,6 +354,6 @@ process fastqc {
     ulimit -a >>${repRID}.fastqc.err
 
     # run fastqc
-    fastqc *.fastq.gz >>${repRID}.fastqc.err
+    fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
     """
 }
\ No newline at end of file