From ba58c6504e9fd9d3945edf5f2b59e7604fae263b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 23 Feb 2021 21:59:06 -0600
Subject: [PATCH] Fix ci lint
---
.gitlab-ci.yml | 49 ++++++++++++++++++++++++-------------------------
1 file changed, 24 insertions(+), 25 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8df331b..8dd2e7a 100644
--- a/.gitlab-ci.yml
+++ b/.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
--
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