Change singularity run to exec

.gitlab-ci.yml

@@ -42,7 +42,7 @@ astrocyte_check:
     refs:
       - tags
   script:
-    - singularity run 'docker://bicf/cellranger2.1.1:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2
+    - singularity exec 'docker://bicf/cellranger2.1.1:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2
   retry:
     max: 1
     when:
@@ -56,7 +56,7 @@ astrocyte_check:
     refs:
       - tags
   script:
-    - singularity run 'docker://bicf/cellranger2.2.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2
+    - singularity exec 'docker://bicf/cellranger2.2.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2
   retry:
     max: 1
     when:
@@ -70,7 +70,7 @@ astrocyte_check:
     refs:
       - tags
   script:
-    - singularity run 'docker://bicf/cellranger3.0.2:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2 --chemistry=SC3Pv2
+    - singularity exec 'docker://bicf/cellranger3.0.2:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2 --chemistry=SC3Pv2
   retry:
     max: 1
     when:
@@ -84,7 +84,7 @@ astrocyte_check:
     refs:
       - tags
   script:
-    - singularity run 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2 --chemistry=SC3Pv2
+    - singularity exec 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=test_data/hu.v2s1r500/*.fastq.gz --sample=pbmc_1k_v2 --chemistry=SC3Pv2
   retry:
     max: 1
     when: