diff --git a/.gitignore b/.gitignore index a42ce01..b20e6de 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ testing/ testing* *.pyc null/ +.singularityCache/ diff --git a/main.nf b/main.nf index 531179b..5edf324 100644 --- a/main.nf +++ b/main.nf @@ -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' diff --git a/modules/nf-core/bfconvert/main.nf b/modules/nf-core/bfconvert/main.nf index 59382e4..deabbaa 100644 --- a/modules/nf-core/bfconvert/main.nf +++ b/modules/nf-core/bfconvert/main.nf @@ -1,4 +1,4 @@ -nextflow.enable.moduleBinaries = true +//nextflow.enable.moduleBinaries = true // TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) // https://github.com/nf-core/modules/tree/master/modules/nf-core/ // You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: diff --git a/nextflow.config b/nextflow.config index b987150..334eb40 100644 --- a/nextflow.config +++ b/nextflow.config @@ -28,7 +28,8 @@ params { bigtiff = null pyramid_resolutions = null pyramid_scale = null - // singularityCache = "${baseDir}/.singularityCache" + singularityCache = "/dodrio/scratch/projects/2024_300/twoller/.singularityCache" + cluster_options = "--mem-per-cpu=3140 --cpus-per-task=4 " // Boilerplate options outdir = null @@ -98,8 +99,29 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - //singularity.cacheDir = "${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