Merge branch 'develop' into 'master'

Develop

See merge request !22

.gitlab-ci.yml

 before_script:
+  - module load astrocyte
   - module load python/3.6.1-2-anaconda
   - module load nextflow/0.31.1_Ignite
-  - mkdir test_data/v2s2r100k
-  - mkdir test_data/v3s2r100k
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/* test_data/v2s2r100k/
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/* test_data/v3s2r100k/
+  - mkdir test_data/mu.v2s2r10k
+  - mkdir test_data/hu.v3s2r10k
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
 
 stages:
-  - integration
+  - astrocyte
+  - run
 
-simple_cr2v2ref1.2.0:
-  stage: integration
+astrocyte_check:
+  stage: astrocyte
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - astrocyte_cli check ../cellranger_count
 
-simple_cr2v2ref3.0.0:
-  stage: integration
+run_mu.cr2v2ref1.2.0:
+  stage: run
+  except:
+    - tags
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/mu.v2s2r10k/design.csv" --genome 'mm10-1.2.0' --kitVersion 'two' --version '2.1.1'
 
-simple_cr3v2ref3.0.0:
-  stage: integration
+run_hu.cr3v3ref3.0.0:
+  stage: run
+  except:
+    - tags
   script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
-
-simple_cr3v3ref3.0.0:
-  stage: integration
-  script:
-  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v3s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v3s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'

workflow/main.nf

@@ -71,6 +71,7 @@ process checkDesignFile {
   script:
 
   """
+  module load python/3.6.1-2-anaconda
   python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
   """
 }
@@ -123,6 +124,9 @@ process count211 {
   version == '2.1.1'
 
   script:
+  """
+  module load cellranger/2.1.1
+  """
   if (forceCells211 == 0){
     	"""
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
@@ -156,6 +160,9 @@ process count301 {
   version == '3.0.1'
 
   script:
+  """
+  module load cellranger/3.0.1
+  """
   if (forceCells301 == 0){
     	"""
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
@@ -189,6 +196,9 @@ process count302 {
   version == '3.0.2'
 
   script:
+  """
+  module load cellranger/3.0.2
+  """
   if (forceCells302 == 0){
     	"""
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"