Commit a083e6cc authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Layer configs

parent 83282eb9
Pipeline #7333 failed with stages
in 8 seconds
......@@ -27,7 +27,7 @@ astrocyte_check:
simple_1FC:
stage: simple
script:
- nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv"
- nextflow run workflow/main.nf -config biohpc,cluster --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
##- pytest -m simple1
artifacts:
name: "$CI_JOB_NAME"
......@@ -44,7 +44,7 @@ simple_1FC:
simple_2FC:
stage: simple
script:
- nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
- nextflow run workflow/main.nf -config biohpc,cluster --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
##- pytest -m simple2
artifacts:
name: "$CI_JOB_NAME"
......
......@@ -8,9 +8,8 @@ aws {
}
process {
executor = 'awsbatch'
queue = 'default-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
container = 'bicf/bicfbase:1.4'
executor = 'awsbatch'=
container = 'bicf/bicfbase:2.0.0'
cpus = 1
memory = '1 GB'
......
workDir = 's3://gudmap.rbk/work'
aws.client.storageEncryption = 'AES256'
aws {
region = 'us-east-2'
batch {
cliPath = '/home/ec2-user/miniconda/bin/aws'
}
}
process {
executor = 'awsbatch'
queue = 'highpriority-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
container = 'bicf/bicfbase:1.4'
cpus = 1
memory = '1 GB'
withName:checkDesignFile {
container = 'bicf/python3:1.3'
cpus = 4
}
withName:mkfastq {
container = 'bicf/cellranger3.1.0:1.0'
cpus = 6
memory = '2 GB'
}
withName:fastqc {
container = 'bicf/fastqc:1.5'
cpus = 30
memory = '15 GB'
}
withName:versions {
container = 'bicf/python3:1.3'
cpus = 6
}
withName:multiqc {
container = 'bicf/multiqc:1.4'
}
}
\ No newline at end of file
process {
executor = 'slurm'
queue = 'super'
clusterOptions = '--hold'
container = 'docker://bicf/bicfbase:1.4'
container = 'docker://bicf/bicfbase:2.0.0'
withName:trackStart {
executor = 'local'
}
withName:checkDesignFile {
container = 'docker://bicf/python3:1.3'
executor = 'local'
}
withName:untarBCL {
queue = 'super'
}
withName:mkfastq {
container = 'docker://bicf/cellranger3.1.0:1.0'
queue = '128GB,256GB,256GBv1,384GB'
}
withName:countDesign {
executor = 'local'
}
withName:fastqc {
container = 'docker://bicf/fastqc:1.5'
queue = 'super'
}
withName:versions {
container = 'docker://bicf/python3:1.3'
executor = 'local'
}
withName:multiqc {
container = 'docker://bicf/multiqc:1.4'
executor = 'local'
}
}
......
process {
executor = 'local'
container = 'docker://bicf/bicfbase:1.3'
withName:checkDesignFile {
container = 'docker://bicf/python3:1.3'
}
withName:mkfastq {
container = 'docker://bicf/cellranger3.1.0:1.0'
}
withName:fastqc {
container = 'docker://bicf/fastqc:1.5'
}
withName:versions {
container = 'docker://bicf/python3:1.3'
}
withName:multiqc {
container = 'docker://bicf/multiqc:1.4'
}
}
singularity {
enabled = true
cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
}
env {
http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128'
all_proxy = 'http://proxy.swmed.edu:3128'
}
\ No newline at end of file
process {
executor = 'slurm'
queue = 'super'
clusterOptions = '--hold'
withName:trackStart {
executor = 'local'
}
withName:checkDesignFile {
executor = 'local'
}
withName:untarBCL {
queue = 'super'
}
withName:mkfastq {
queue = '128GB,256GB,256GBv1,384GB'
}
withName:countDesign {
executor = 'local'
}
withName:fastqc {
queue = 'super'
}
withName:versions {
executor = 'local'
}
withName:multiqc {
executor = 'local'
}
}
process {
executor = 'local'
}
process {
queue = 'highpriority-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
}
process {
queue = 'default-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
}
......@@ -2,14 +2,20 @@ profiles {
standard {
includeConfig 'configs/biohpc.config'
}
biohpc_local {
includeConfig 'configs/biohpc_local.config'
local {
includeConfig 'configs/local.config'
}
aws_ondemand {
includeConfig 'configs/aws_ondemand.config'
local {
includeConfig 'configs/cluster.config'
}
aws_spot {
includeConfig 'configs/aws_spot.config'
aws {
includeConfig 'configs/aws.config'
}
ondemand {
includeConfig 'configs/ondemand.config'
}
spot {
includeConfig 'configs/spot.config'
}
}
......
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