From 5b0ec09c3883e8be16d62150239a9095eff977c6 Mon Sep 17 00:00:00 2001 From: Jalil Nourisa Date: Wed, 9 Oct 2024 21:25:46 +0200 Subject: [PATCH] scenic+ memory updated --- _viash.yaml | 2 +- src/methods/multi_omics/scenicplus/config.vsh.yaml | 2 +- src/methods/multi_omics/scenicplus/script.py | 3 ++- src/methods/multi_omics/scenicplus_ns/config.vsh.yaml | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/_viash.yaml b/_viash.yaml index 485711e53..ccf697573 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -11,5 +11,5 @@ config_mods: | .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/task_grn_inference' .platforms[.type == "nextflow"].directives.tag := "$id" .platforms[.type == "nextflow"].auto.simplifyOutput := false - .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", onedaytime : "time = 24.h", threedaystime : "time = 72.h", oneweektime : "time = 168.h" } + .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", 250GBmem : "memory = 250.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", onedaytime : "time = 24.h", threedaystime : "time = 72.h", oneweektime : "time = 168.h" } .platforms[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'" \ No newline at end of file diff --git a/src/methods/multi_omics/scenicplus/config.vsh.yaml b/src/methods/multi_omics/scenicplus/config.vsh.yaml index 11a10f147..9ca6fad8e 100644 --- a/src/methods/multi_omics/scenicplus/config.vsh.yaml +++ b/src/methods/multi_omics/scenicplus/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime,midmem,midcpu] + label: [onedaytime,250GBmem,highcpu] diff --git a/src/methods/multi_omics/scenicplus/script.py b/src/methods/multi_omics/scenicplus/script.py index 3b9f66601..876ecbe7b 100644 --- a/src/methods/multi_omics/scenicplus/script.py +++ b/src/methods/multi_omics/scenicplus/script.py @@ -36,8 +36,9 @@ if args.num_workers: par['num_workers'] = args.num_workers -meta = {} + if args.resources_dir: + meta = {} meta['resources_dir'] = args.resources_dir par['num_workers'] = int(par['num_workers']) print(par) diff --git a/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml b/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml index 77e27e2d7..6f7b2107a 100644 --- a/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml +++ b/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml @@ -40,4 +40,4 @@ functionality: platforms: - type: nextflow directives: - label: [ onedaytime, highmem, highcpu ] + label: [ onedaytime, 250GBmem, highcpu ]