Set default queue to 32GB and fix CI for new runner settings

.gitlab-ci.yml

@@ -22,7 +22,7 @@ stages:
 astrocyte_check:
   stage: astrocyte
   script:
-    - astrocyte_cli check ../cellranger_count
+    - astrocyte_cli check .
   artifacts:
     expire_in: 2 days
   retry:
@@ -40,7 +40,7 @@ simple_1:
       - develop
       - master
   script:
-  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
+  - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -65,7 +65,7 @@ simple_2:
       - master
       - tags
   script:
-  - nextflow run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
+  - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.1.0' -with-tower
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"

README.md

 |*master*|*develop*|
 |:-:|:-:|
-|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/master)|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/develop/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/develop)|
+|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/master)|[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/badges/develop/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/commits/develop)|
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2652622.svg)](https://doi.org/10.5281/zenodo.2652622)
 

workflow/conf/biohpc_cluster.config

 process {
   executor = 'slurm'
-  queue = 'super'
+  queue = '32GB'
   clusterOptions = '--hold'
 
   withLabel: checkDesignFile {
@@ -31,4 +31,4 @@ process {
     module = ['multiqc/1.7']
     executor = 'local'
   }
-}
\ No newline at end of file
+}

workflow/main.nf

@@ -332,7 +332,6 @@ metricsSummary = metricsSummary211.mix(metricsSummary301, metricsSummary302, met
 process multiqc {
 
   tag "${name}"
-  queue 'super'
   publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
   module 'multiqc/1.7'