Update .gitlab-ci.yml

.gitlab-ci.yml

@@ -71,7 +71,7 @@ dedupData:
   - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
   - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' "
       for i in {chr1,chr2,chr8}; do
-        echo \"samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ \`nproc\` -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai\"; done | parallel -j `nproc` -k
+        echo \"samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam \${i} > Q-Y5JA_1M.se.sorted.deduped.\${i}.bam; samtools index -@ \`nproc\` -b Q-Y5JA_1M.se.sorted.deduped.\${i}.bam Q-Y5JA_1M.se.sorted.deduped.\${i}.bam.bai\"; done | parallel -j `nproc` -k
         "
   - pytest -m dedupData