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POC on HPC VSC #1

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POC on HPC VSC #1

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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
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1 change: 1 addition & 0 deletions .gitignore
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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
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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'
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2 changes: 1 addition & 1 deletion modules/nf-core/bfconvert/main.nf
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28 changes: 25 additions & 3 deletions nextflow.config
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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
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