Fix spike override test

.gitlab-ci.yml

@@ -792,13 +792,13 @@ override_inputBag:
   - hostname
   - ulimit -a
   - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename inputBagOverride_PE_multiqc_data.json
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_multiqc_data.json \;
+  - pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
     paths:
-      - inputBagOverride_PE_multiqc_data.json
+      - inputBagOverride_multiqc_data.json
     expire_in: 7 days
   retry:
     max: 0
@@ -815,13 +815,13 @@ override_fastq:
   - hostname
   - ulimit -a
   - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename fastqOverride_PE_multiqc_data.json
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
+  - pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
     paths:
-      - fastqOverride_PE_multiqc_data.json
+      - fastqOverride_multiqc_data.json
     expire_in: 7 days
   retry:
     max: 0
@@ -838,13 +838,13 @@ override_species:
   - hostname
   - ulimit -a
   - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename speciesOverride_PE_multiqc_data.json
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
+  - pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
     paths:
-      - speciesOverride_PE_multiqc_data.json
+      - speciesOverride_multiqc_data.json
     expire_in: 7 days
   retry:
     max: 0
@@ -861,13 +861,13 @@ override_stranded:
   - hostname
   - ulimit -a
   - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_PE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename strandedOverride_PE_multiqc_data.json
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
+  - pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
     paths:
-      - strandedOverride_PE_multiqc_data.json
+      - strandedOverride_multiqc_data.json
     expire_in: 7 days
   retry:
     max: 0
@@ -884,13 +884,13 @@ override_spike:
   - hostname
   - ulimit -a
   - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce t --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
-  - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_PE_multiqc_data.json \;
-  - pytest -m completionMultiqc --filename spikedOverride_PE_multiqc_data.json
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
+  - pytest -m completionMultiqc --filename spikeOverride_multiqc_data
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
     paths:
-      - spikedOverride_PE_multiqc_data.json
+      - spikedOverride_multiqc_data.json
     expire_in: 7 days
   retry:
     max: 0