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Update scanpy GPU image #130

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merged 4 commits into from
Nov 13, 2024
Merged

Update scanpy GPU image #130

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649986b
Update scanpy GPU image
nictru Nov 12, 2024
367246b
Switch to new way of GPU profile
nictru Nov 13, 2024
e944a64
Set a cupy cache dir
nictru Nov 13, 2024
68ac45e
Move "withLabel" to base.config
nictru Nov 13, 2024
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4 changes: 2 additions & 2 deletions conf/base.config
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Expand Up @@ -52,8 +52,8 @@ process {
withLabel:process_high_memory {
memory = { 200.GB * task.attempt * params.memory_scale }
}
withLabel:process_gpu {
ext.use_gpu = { use_gpu }
withLabel: process_gpu {
ext.use_gpu = {workflow.profile.contains('gpu')}
}
withLabel:error_ignore {
errorStrategy = 'ignore'
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2 changes: 1 addition & 1 deletion modules/local/scanpy/harmony/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_HARMONY {
label 'process_gpu'

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/harmonypy_scanpy:25dd7b6ef4c76098':
'community.wave.seqera.io/library/harmonypy_scanpy:e9c9a621297da9ea' }"
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2 changes: 1 addition & 1 deletion modules/local/scanpy/hvgs/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_HVGS {
label 'process_gpu'

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/python-igraph_scanpy:a7114d55b0af3893':
'community.wave.seqera.io/library/python-igraph_scanpy:5f677450e42211ef' }"
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2 changes: 1 addition & 1 deletion modules/local/scanpy/leiden/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_LEIDEN {
// label 'process_gpu' Issue: https://github.com/scverse/rapids_singlecell/issues/286

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/leidenalg_python-igraph_scanpy:4c35b8e384d7de2d':
'community.wave.seqera.io/library/leidenalg_python-igraph_scanpy:ba212a162d290cb6' }"
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2 changes: 1 addition & 1 deletion modules/local/scanpy/neighbors/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_NEIGHBORS {
label 'process_gpu'

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/python-igraph_scanpy:a7114d55b0af3893':
'community.wave.seqera.io/library/python-igraph_scanpy:5f677450e42211ef' }"
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2 changes: 1 addition & 1 deletion modules/local/scanpy/rankgenesgroups/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_RANKGENESGROUPS {
label 'process_gpu'

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/scanpy:1.10.1--ea08051addf267ac':
'community.wave.seqera.io/library/scanpy:1.10.1--0c8c97148fc05558' }"
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2 changes: 2 additions & 0 deletions modules/local/scanpy/rankgenesgroups/templates/rank_genes_groups.py
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Expand Up @@ -48,6 +48,8 @@ def format_yaml_like(data: dict, indent: int = 0) -> str:

if adata.obs["${obs_key}"].value_counts().size > 1:
if use_gpu:
os.environ["CUPY_CACHE_DIR"] = "./tmp/cupy"

import rapids_singlecell as rsc
import rmm
from rmm.allocators.cupy import rmm_cupy_allocator
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2 changes: 1 addition & 1 deletion modules/local/scanpy/scrublet/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_SCRUBLET {
label 'process_gpu'

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/scanpy_scikit-image:185956e1b73ad93d':
'community.wave.seqera.io/library/scanpy_scikit-image:066cc4cb329a805c' }"
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2 changes: 1 addition & 1 deletion modules/local/scanpy/umap/main.nf
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Expand Up @@ -4,7 +4,7 @@ process SCANPY_UMAP {
label 'process_gpu'

conda "${moduleDir}/environment.yml"
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.8' :
container "${ task.ext.use_gpu ? 'ghcr.io/scverse/rapids_singlecell:v0.10.11' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/scanpy:1.10.1--ea08051addf267ac':
'community.wave.seqera.io/library/scanpy:1.10.1--0c8c97148fc05558' }"
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7 changes: 3 additions & 4 deletions nextflow.config
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Expand Up @@ -176,10 +176,9 @@ profiles {
executor.memory = 8.GB
}
gpu {
docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
apptainer.runOptions = '--nv'
singularity.runOptions = '--nv'
use_gpu = true
docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
apptainer.runOptions = '--nv'
singularity.runOptions = '--nv'
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
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