diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1e339716c435f74c0cf4d60eb083499f81e3ae5a..f3b389f4071fa6aedf10a70f76c127343cd28f49 100755
--- a/.gitlab-ci.yml
+++ b/.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'
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index e96cb4e5a55717bed78238ee74c712b4f27826ac..8417664465fb8691f52e97960b6acda0b54594c8 100755
--- a/astrocyte_pkg.yml
+++ b/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: []
diff --git a/workflow/main.nf b/workflow/main.nf
index 82d30dfbfb02aae0ba5cbaadac9fb0a8b9302ccc..3649ddfcc70460d5142e3c39cc3b803396c4fe25 100755
--- a/workflow/main.nf
+++ b/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