Skip to content

POC on HPC VSC #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
tatianawoller wants to merge 5 commits into
base: main
Choose a base branch
from
Open

POC on HPC VSC #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
d4ba4f1
Update .gitignore
tatianawoller Dec 5, 2024
a51a32c
change HPC VSC with Bugra
tatianawoller Dec 5, 2024
98de69d
Delete bfflow directory
tatianawoller Dec 5, 2024
1286230
modification bfflow for HPC VSC with bugra
tatianawoller Dec 5, 2024
a55ba9e
nextflow.config not using institutional config
tatianawoller Dec 5, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,4 @@ testing/
testing*
*.pyc
null/
.singularityCache/
2 changes: 1 addition & 1 deletion main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
nextflow.enable.moduleBinaries = true
//nextflow.enable.moduleBinaries = true

include { BATCHCONVERT_TO_OMETIFF } from './workflows/bftools.nf'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_demo_workflow_pipeline'
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/bfconvert/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

28 changes: 25 additions & 3 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@ params {
bigtiff = null
pyramid_resolutions = null
pyramid_scale = null
// singularityCache = "${baseDir}/.singularityCache"
singularityCache = "/dodrio/scratch/projects/2024_300/twoller/.singularityCache"
cluster_options = "--mem-per-cpu=3140 --cpus-per-task=4 "

// Boilerplate options
outdir = null
Expand Down Expand Up @@ -98,8 +99,29 @@ profiles {
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
//singularity.cacheDir = "${params.singularityCache}"

singularity.cacheDir = "${params.singularityCache}"
singularity.autoMounts = true
process {
executor = 'local'
containerOptions = "-B ${baseDir} -B $PWD -B $HOME"
}
}
cluster {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
singularity.cacheDir = "${params.singularityCache}"
singularity.autoMounts = true
process {
executor = 'slurm'
clusterOptions = "${params.cluster_options}"
containerOptions = "-B ${baseDir} -B $PWD -B $HOME"
}
}
podman {
podman.enabled = true
Expand Down