Cleanup some ci misses

.gitignore

@@ -298,4 +298,4 @@ timeline*.html*
 *.out
 run*.sh
 
-!.gitkeep
+!.gitkeep
\ No newline at end of file

.gitlab-ci.yml

@@ -51,7 +51,7 @@ trimData:
 alignData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bai

workflow/rna-seq.nf

@@ -234,7 +234,7 @@ process getRef {
 */
 process trimData {
   tag "${repRID}"
-  publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.trimData.*"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.trimData.*"
 
   input:
     val endsManual_trimData
@@ -266,7 +266,6 @@ process trimData {
 */
 process alignData {
   tag "${repRID}"
-  publishDir "${outDir}/alignData", mode: "copy", pattern: "*.{bam,bai}"
   publishDir "${logsDir}", mode: "copy", pattern: "*.align.{out,err}"
 
   input:

workflow/tests/test_alignReads.py

@@ -7,8 +7,6 @@ import utils
 
 data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 	'/../../'
-logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-	'/../../'
 
 
 @pytest.mark.alignData
@@ -27,15 +25,15 @@ def test_alignData_pe():
 
 @pytest.mark.alignLogs
 def test_alignLogs_se():
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.err'))
-	assert '34497376 reads; of these:' in open(os.path.join(logs_output_path, '16-1ZX4.align.err')).readlines()[0]
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.out'))
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.align.err'))
+	assert '34497376 reads; of these:' in open(os.path.join(data_output_path, '16-1ZX4.align.err')).readlines()[0]
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.align.out'))
 
 
 @pytest.mark.alignLogs
 def test_alignLogs_pe():
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.err'))
-	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.err')) == 7
-	assert '15824858 reads; of these:' in open(os.path.join(logs_output_path, 'Q-Y5JA.align.err')).readlines()[0]
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.out'))
-	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.out')) == 0
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.align.err'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.align.err')) == 7
+	assert '15824858 reads; of these:' in open(os.path.join(data_output_path, 'Q-Y5JA.align.err')).readlines()[0]
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.align.out'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.align.out')) == 0