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Commit e1d62b1f authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Merge branch 'develop' into 'master'

Develop

See merge request !28
parents d275028d b69acc56
2 merge requests!64Master,!28Develop
Pipeline #3326 passed with stages
in 4 minutes and 36 seconds
...@@ -2,30 +2,38 @@ before_script: ...@@ -2,30 +2,38 @@ before_script:
- module load astrocyte - module load astrocyte
- module load python/3.6.1-2-anaconda - module load python/3.6.1-2-anaconda
- module load nextflow/0.31.1_Ignite - module load nextflow/0.31.1_Ignite
- mkdir test_data/hu.v2s1r500
- mkdir test_data/mu.v2s2r10k - mkdir test_data/mu.v2s2r10k
- mkdir test_data/hu.v3s2r10k - 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/mu.v2s2r10k/* test_data/mu.v2s2r10k/
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/ - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
stages: stages:
- astrocyte - astrocyte
- run - simple
- detailed
astrocyte_check: astrocyte_check:
stage: astrocyte stage: astrocyte
script: script:
- astrocyte_cli check ../cellranger_count - 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: run_mu.cr2v2ref1.2.0:
stage: run stage: detailed
except: except:
- tags - tags
script: 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: run_hu.cr3v3ref3.0.0:
stage: run stage: detailed
except: except:
- tags - tags
script: 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'
...@@ -177,5 +177,4 @@ vizapp_cran_packages: ...@@ -177,5 +177,4 @@ vizapp_cran_packages:
# List of any Bioconductor packages, not provided by the modules, # List of any Bioconductor packages, not provided by the modules,
# that must be made available to the vizapp # that must be made available to the vizapp
vizapp_bioc_packages: vizapp_bioc_packages: []
- chipseq
...@@ -7,12 +7,9 @@ ...@@ -7,12 +7,9 @@
params.fastq = "$baseDir/../test_data/*.fastq.gz" params.fastq = "$baseDir/../test_data/*.fastq.gz"
params.designFile = "$baseDir/../test_data/design.csv" params.designFile = "$baseDir/../test_data/design.csv"
params.genome = 'GRCh38-3.0.0' params.genome = 'GRCh38-3.0.0'
params.expectCells = 10000 params.expectCells = 10000
params.forceCells = 0 params.forceCells = 0
params.kitVersion = 'three' params.kitVersion = 'three'
params.version = '3.0.2' params.version = '3.0.2'
params.astrocyte = false params.astrocyte = false
params.outDir = "$baseDir/output" params.outDir = "$baseDir/output"
...@@ -35,7 +32,6 @@ if (params.astrocyte) { ...@@ -35,7 +32,6 @@ if (params.astrocyte) {
params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
params.chemistry = [] params.chemistry = []
params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
} }
params.genomeLocationFull = params.genomeLocation+params.genome params.genomeLocationFull = params.genomeLocation+params.genome
...@@ -128,21 +124,20 @@ process count211 { ...@@ -128,21 +124,20 @@ process count211 {
version == '2.1.1' version == '2.1.1'
script: script:
"""
module load cellranger/2.1.1
"""
if (forceCells211 == 0){ if (forceCells211 == 0){
""" """
hostname hostname
ulimit -a ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211 module load cellranger/2.1.1
""" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
"""
} else { } else {
""" """
hostname hostname
ulimit -a ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211 module load cellranger/2.1.1
""" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
"""
} }
} }
...@@ -168,21 +163,20 @@ process count301 { ...@@ -168,21 +163,20 @@ process count301 {
version == '3.0.1' version == '3.0.1'
script: script:
"""
module load cellranger/3.0.1
"""
if (forceCells301 == 0){ if (forceCells301 == 0){
""" """
hostname hostname
ulimit -a ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301" module load cellranger/3.0.1
""" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
"""
} else { } else {
""" """
hostname hostname
ulimit -a ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301" module load cellranger/3.0.1
""" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
"""
} }
} }
...@@ -208,20 +202,19 @@ process count302 { ...@@ -208,20 +202,19 @@ process count302 {
version == '3.0.2' version == '3.0.2'
script: script:
"""
module load cellranger/3.0.2
"""
if (forceCells302 == 0){ if (forceCells302 == 0){
""" """
hostname hostname
ulimit -a ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302" module load cellranger/3.0.2
""" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
"""
} else { } else {
""" """
hostname hostname
ulimit -a ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302" module load cellranger/3.0.2
""" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
"""
} }
} }
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