Corrected CI file.

.gitlab-ci.yml

@@ -45,14 +45,14 @@ trimData:
 alignReads:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA.unal.gz -S Q-Y5JA.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 Q-Y5JA_R1_val_1.fq.gz -2 Q-Y5JA_R2_val_2.fq.gz 1>Q-Y5JA.align.out 2>Q-Y5JA.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA.bam Q-Y5JA.sam 1>>Q-Y5JA.align.out 2>>Q-Y5JA.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA.sorted.bam Q-Y5JA.bam 1>>Q-Y5JA.align.out 2>>Q-Y5JA.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA.sorted.bam Q-Y5JA.sorted.bai 1>>Q-Y5JA.align.out 2>>Q-Y5JA.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz 16-1ZX4.unal.gz -S 16-1ZX4.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U 16-1ZX4_trimmed.fq.gz 1>16-1ZX4.align.out 2>16-1ZX4.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o 16-1ZX4.bam 16-1ZX4.sam 1>>16-1ZX4.align.out 2>>16-1ZX4.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o 16-1ZX4.sorted.bam 16-1ZX4.bam 1>>16-1ZX4.align.out 2>>16-1ZX4.align.err
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b 16-1ZX4.sorted.bam 16-1ZX4.sorted.bai 1>>16-1ZX4.align.out 2>>16-1ZX4.align.err
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz ./test_data/fastq/Q-Y5JA.unal.gz -S ./test_data/fastq/Q-Y5JA.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/Q-Y5JA_R1_val_1.fq.gz -2 ./test_data/fastq/Q-Y5JA_R2_val_2.fq.gz
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ./test_data/fastq/Q-Y5JA.bam ./test_data/fastq/Q-Y5JA.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/fastq/Q-Y5JA.sorted.bam ./test_data/fastq/Q-Y5JA.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b ./test_data/fastq/Q-Y5JA.sorted.bam ./test_data/fastq/Q-Y5JA.sorted.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz ./test_data/fastq/16-1ZX4.unal.gz -S ./test_data/fastq/16-1ZX4.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U ./test_data/fastq/16-1ZX4_trimmed.fq.gz
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ./test_data/fastq/16-1ZX4.bam ./test_data/fastq/16-1ZX4.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/fastq/16-1ZX4.sorted.bam ./test_data/fastq/16-1ZX4.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b ./test_data/fastq/16-1ZX4.sorted.bam ./test_data/fastq/16-1ZX4.sorted.bai
   - pytest -m alignReads
 
 integration_se: