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Commit 17fe1fd5 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Revert to layered configs

parent 40116fcc
2 merge requests!63Develop,!60Resolve "Add 3':5' param"
Pipeline #6540 canceled with stages
in 34 minutes and 1 second
...@@ -40,7 +40,7 @@ simple_1: ...@@ -40,7 +40,7 @@ simple_1:
- develop - develop
- master - master
script: script:
- nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
- pytest -m count310 - pytest -m count310
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -65,7 +65,7 @@ simple_2: ...@@ -65,7 +65,7 @@ simple_2:
- master - master
- tags - tags
script: script:
- nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
- pytest -m count310 - pytest -m count310
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -89,7 +89,7 @@ detailed_1: ...@@ -89,7 +89,7 @@ detailed_1:
refs: refs:
- tags - tags
script: script:
- nextflow -q run workflow/main.nf -profile biohpc,_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0' - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
- pytest -m count310 - pytest -m count310
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -114,7 +114,7 @@ detailed_2: ...@@ -114,7 +114,7 @@ detailed_2:
refs: refs:
- tags - tags
script: script:
- nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2' - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
- pytest -m count302 - pytest -m count302
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -138,7 +138,7 @@ detailed_3: ...@@ -138,7 +138,7 @@ detailed_3:
refs: refs:
- tags - tags
script: script:
- nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1' - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
- pytest -m count301 - pytest -m count301
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
...@@ -162,7 +162,7 @@ detailed_4: ...@@ -162,7 +162,7 @@ detailed_4:
refs: refs:
- tags - tags
script: script:
- nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1' - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
- pytest -m count211 - pytest -m count211
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
......
process {
executor = 'local'
withLabel: checkDesignFile {
module = ['python/3.6.1-2-anaconda']
}
withLabel: count211 {
module = ['cellranger/2.1.1']
}
withLabel: count301 {
module = ['cellranger/3.0.1']
}
withLabel: count302 {
module = ['cellranger/3.0.2']
}
withLabel: count310 {
module = ['cellranger/3.1.0']
}
withLabel: versions {
module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
}
withLabel: multiqc {
module = ['multiqc/1.7']
}
}
params { params {
// Reference file paths on BioHPC // Reference file paths on BioHPC
genomes { genomes {
......
...@@ -5,7 +5,6 @@ process { ...@@ -5,7 +5,6 @@ process {
withLabel: checkDesignFile { withLabel: checkDesignFile {
module = ['python/3.6.1-2-anaconda'] module = ['python/3.6.1-2-anaconda']
queue = '32GB'
} }
withLabel: count211 { withLabel: count211 {
module = ['cellranger/2.1.1'] module = ['cellranger/2.1.1']
...@@ -25,64 +24,8 @@ process { ...@@ -25,64 +24,8 @@ process {
} }
withLabel: versions { withLabel: versions {
module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7'] module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
queue = '32GB'
} }
withLabel: multiqc { withLabel: multiqc {
module = ['multiqc/1.7'] module = ['multiqc/1.7']
queue = '32GB'
}
}
params {
// Reference file paths on BioHPC
genomes {
'GRCh38-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'GRCh38-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'hg19-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'hg19-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'mm10-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'mm10-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'GRCh38_and_mm10-3.1.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'hg19_and_mm10-3.0.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'hg19_and_mm10-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
'ercc92-1.2.0' {
loc = '/project/apps_database/cellranger/refdata-cellranger-'
}
}
// Chemistry mapping parameter
chemistry {
'auto' {
param = 'auto'
}
'3GEXv1' {
param = 'SC3Pv1'
}
'3GEXv2' {
param = 'SC3Pv2'
}
'3GEXv3' {
param = 'SC3Pv3'
}
'5GEX' {
param = 'fiveprime'
}
} }
} }
process {
executor = 'local'
withLabel: checkDesignFile {
module = ['python/3.6.1-2-anaconda']
}
withLabel: count211 {
module = ['cellranger/2.1.1']
}
withLabel: count301 {
module = ['cellranger/3.0.1']
}
withLabel: count302 {
module = ['cellranger/3.0.2']
}
withLabel: count310 {
module = ['cellranger/3.1.0']
}
withLabel: versions {
module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
}
withLabel: multiqc {
module = ['multiqc/1.7']
}
}
profiles { profiles {
biohpc_local { biohpc {
includeConfig 'conf/biohpc_local.config' includeConfig 'conf/biohpc.config'
} }
biohpc_cluster { local {
includeConfig 'conf/biohpc_cluster.config' includeConfig 'conf/local.config'
}
cluster {
includeConfig 'conf/cluster.config'
} }
aws { aws {
includeConfig 'conf/aws.config' includeConfig 'conf/aws.config'
......
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