Fix ci lint

.gitlab-ci.yml

@@ -162,7 +162,6 @@ seqwho:
       - version_seqwho.txt
     expire_in: 7 days
 
-
 trimData:
   stage: unit
   only:
@@ -197,30 +196,30 @@ downsampleData:
   - singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
   - pytest -m downsampleData
 
-  inferMetadata:
-    stage: unit
-    only:
-      - push
-      - tags
-    except:
-      - merge_requests
-      - schedules
-    script:
-    - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
-    - >
-      align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
-      if [[ ${align} == "" ]]; then exit 1; fi
-    - >
-      singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
-      ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
-      if [[ ${ended} == "" ]]; then exit 1; fi
-    - pytest -m inferMetadata
-    artifacts:
-      name: "$CI_JOB_NAME"
-      when: always
-      paths:
-        - version_rseqc.txt
-      expire_in: 7 days
+inferMetadata:
+  stage: unit
+  only:
+    - push
+    - tags
+  except:
+    - merge_requests
+    - schedules
+  script:
+  - singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
+  - >
+    align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
+    if [[ ${align} == "" ]]; then exit 1; fi
+  - >
+    singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/new/GRCh38.p13.v36/data/annotation/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
+    ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
+    if [[ ${ended} == "" ]]; then exit 1; fi
+  - pytest -m inferMetadata
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - version_rseqc.txt
+    expire_in: 7 days
   
 alignData:
   stage: unit