Add chemistry flag to all cellranger processes

.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 --sample=pbmc_1k_v2
+    - 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 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
   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 --sample=pbmc_1k_v2
+    - 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 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
   retry:
     max: 1
     when:

workflow/main.nf

@@ -132,6 +132,8 @@ forceCells211 = forceCells
 forceCells220 = forceCells
 forceCells302 = forceCells
 forceCells310 = forceCells
+chemistryParam211 = chemistryParam
+chemistryParam220 = chemistryParam
 chemistryParam302 = chemistryParam
 chemistryParam310 = chemistryParam
 
@@ -149,6 +151,7 @@ process count211 {
     file ref from refLocation211.first()
     expectCells211
     forceCells211
+    chemistryParam211
 
   output:
     file("**/outs/**") into outPaths211
@@ -163,7 +166,7 @@ process count211 {
       hostname
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
-      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211}
+      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211} --chemistry=${chemistryParam211}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     } 
@@ -172,7 +175,7 @@ process count211 {
       hostname
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
-      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211}
+      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211} --chemistry=${chemistryParam211}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     }
@@ -192,6 +195,7 @@ process count220 {
     file ref from refLocation220.first()
     expectCells220
     forceCells220
+    chemistryParam220
 
   output:
     file("**/outs/**") into outPaths220
@@ -251,7 +255,7 @@ process count302 {
       ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
-      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells302}
+      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells302} --chemistry=${chemistryParam302}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     } 
@@ -261,7 +265,7 @@ process count302 {
       ulimit -u 16384
       ulimit -a
       bash ${baseDir}/scripts/filename_check.sh -r ${ref}
-      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells302}
+      cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells302} --chemistry=${chemistryParam302}
       sed -E 's/("([^"]*)")?(,|\$)/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
       """
     }