Merge branch 'develop' into 'master'

Develop

See merge request !28

.gitlab-ci.yml

@@ -2,30 +2,38 @@ before_script:
   - module load astrocyte
   - module load python/3.6.1-2-anaconda
   - module load nextflow/0.31.1_Ignite
+  - mkdir test_data/hu.v2s1r500
   - mkdir test_data/mu.v2s2r10k
   - mkdir test_data/hu.v3s2r10k
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
   - 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:
   - astrocyte
-  - run
+  - simple
+  - detailed
 
 astrocyte_check:
   stage: astrocyte
   script:
   - astrocyte_cli check ../cellranger_count
 
+run_hu.cr3v2ref3.0.0:
+  stage: simple
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/hu.v2s1r500/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/hu.v2s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
+
 run_mu.cr2v2ref1.2.0:
-  stage: run
+  stage: detailed
   except:
     - tags
   script:
-  - 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'
+  - 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 'auto' --version '2.1.1'
 
 run_hu.cr3v3ref3.0.0:
-  stage: run
+  stage: detailed
   except:
     - tags
   script:
-  - 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'
+  - 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 'auto' --version '3.0.2'

astrocyte_pkg.yml

@@ -177,5 +177,4 @@ vizapp_cran_packages:
 
 # List of any Bioconductor packages, not provided by the modules,
 # that must be made available to the vizapp
-vizapp_bioc_packages:
-  - chipseq
+vizapp_bioc_packages: []

workflow/main.nf

@@ -7,12 +7,9 @@
 params.fastq = "$baseDir/../test_data/*.fastq.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
 params.genome = 'GRCh38-3.0.0'
-
-
 params.expectCells = 10000
 params.forceCells = 0
 params.kitVersion = 'three'
-
 params.version = '3.0.2'
 params.astrocyte = false
 params.outDir = "$baseDir/output"
@@ -35,7 +32,6 @@ if (params.astrocyte) {
   params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
   params.chemistry = []
   params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
-
 }
 params.genomeLocationFull = params.genomeLocation+params.genome
 
@@ -128,21 +124,20 @@ process count211 {
   version == '2.1.1'
 
   script:
-  """
-  module load cellranger/2.1.1
-  """
   if (forceCells211 == 0){
-    	"""
-	hostname
-    	ulimit -a
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
-    	"""
+    """
+	  hostname
+    ulimit -a
+    module load cellranger/2.1.1
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
+    """
   } else {
-    	"""
-	hostname
-    	ulimit -a
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
-    	"""
+    """
+	  hostname
+    ulimit -a
+    module load cellranger/2.1.1
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
+    """
   }
 }
 
@@ -168,21 +163,20 @@ process count301 {
   version == '3.0.1'
 
   script:
-  """
-  module load cellranger/3.0.1
-  """
   if (forceCells301 == 0){
-    	"""
-	hostname
-    	ulimit -a
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
-    	"""
+    """
+	  hostname
+    ulimit -a
+    module load cellranger/3.0.1
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
+    """
   } else {
-    	"""
-	hostname
-    	ulimit -a
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
-    	"""
+    """
+	  hostname
+    ulimit -a
+    module load cellranger/3.0.1
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
+    """
   }
 }
 
@@ -208,20 +202,19 @@ process count302 {
   version == '3.0.2'
 
   script:
-  """
-  module load cellranger/3.0.2
-  """
   if (forceCells302 == 0){
-    	"""
-	hostname
-    	ulimit -a
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
-    	"""
+    """
+	  hostname
+    ulimit -a
+    module load cellranger/3.0.2
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
+    """
   } else {
-    	"""
-	hostname
-    	ulimit -a
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
-    	"""
+    """
+	  hostname
+    ulimit -a
+    module load cellranger/3.0.2
+    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
+    """
   }
-}
+}
\ No newline at end of file