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BICF
Astrocyte
cellranger_mkfastq
Commits
a083e6cc
Commit
a083e6cc
authored
Jun 20, 2020
by
Gervaise Henry
🤠
Browse files
Layer configs
parent
83282eb9
Pipeline
#7333
failed with stages
in 8 seconds
Changes
10
Pipelines
1
Hide whitespace changes
Inline
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.gitlab-ci.yml
View file @
a083e6cc
...
...
@@ -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"
...
...
workflow/configs/aws
_spot
.config
→
workflow/configs/aws.config
View file @
a083e6cc
...
...
@@ -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'
...
...
workflow/configs/aws_ondemand.config
deleted
100644 → 0
View file @
83282eb9
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
workflow/configs/biohpc.config
View file @
a083e6cc
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'
}
}
...
...
workflow/configs/biohpc_local.config
deleted
100644 → 0
View file @
83282eb9
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
workflow/configs/cluster.config
0 → 100755
View file @
a083e6cc
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'
}
}
workflow/configs/local.config
0 → 100644
View file @
a083e6cc
process
{
executor
=
'local'
}
workflow/configs/ondemand.config
0 → 100644
View file @
a083e6cc
process
{
queue
=
'highpriority-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
}
workflow/configs/spot.config
0 → 100644
View file @
a083e6cc
process
{
queue
=
'default-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
}
workflow/nextflow.config
View file @
a083e6cc
...
...
@@ -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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