Build branch fix-integration-tests with version fix-integration-tests (c1fe2a62)
Build pipeline: vsh-ci-dev-rdkgl
Source commit: c1fe2a629d
Source message: Update CHANGELOG
This commit is contained in:
CI
@@ -173,6 +173,8 @@
|
||||
|
||||
* `convert/from_10xh5_to_h5mu`: add .uns slot to mdata root when metrics file is provided (PR #887).
|
||||
|
||||
* Use `params.resources_test` in test workflows in order to point to an alternative location (e.g. a cache).
|
||||
|
||||
## DOCUMENTATION
|
||||
|
||||
* Update authorship of components (PR #835).
|
||||
|
||||
@@ -1,7 +1,5 @@
|
||||
viash_version: 0.9.0
|
||||
|
||||
version: dev
|
||||
|
||||
source: src
|
||||
target: target
|
||||
|
||||
|
||||
@@ -1,427 +0,0 @@
|
||||
name: "celltypist"
|
||||
namespace: "annotate"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Jakub Majercik"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "jakub@data-intuitive.com"
|
||||
github: "jakubmajercik"
|
||||
linkedin: "jakubmajercik"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatics Engineer"
|
||||
- name: "Weiwei Schultz"
|
||||
roles:
|
||||
- "contributor"
|
||||
info:
|
||||
role: "Contributor"
|
||||
organizations:
|
||||
- name: "Janssen R&D US"
|
||||
role: "Associate Director Data Sciences"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Input dataset (query) arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "The input (query) data to be labeled. Should be a .h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_layer"
|
||||
description: "The layer in the input data to be used for cell type annotation\
|
||||
\ if .X is not to be used."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--var_query_gene_names"
|
||||
description: "The name of the adata var column in the input data containing gene\
|
||||
\ names; when no gene_name_layer is provided, the var index will be used.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Reference"
|
||||
description: "Arguments related to the reference dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--reference"
|
||||
description: "The reference data to train the CellTypist classifiers on. Only\
|
||||
\ required if a pre-trained --model is not provided."
|
||||
info: null
|
||||
example:
|
||||
- "reference.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_layer"
|
||||
description: "The layer in the reference data to be used for cell type annotation\
|
||||
\ if .X is not to be used. Data are expected to be processed in the same way\
|
||||
\ as the --input query dataset."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_target"
|
||||
description: "The name of the adata obs column in the reference data containing\
|
||||
\ cell type annotations."
|
||||
info: null
|
||||
default:
|
||||
- "cell_ontology_class"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--check_expression"
|
||||
description: "Whether to check the expression of the reference dataset to the\
|
||||
\ format reccomended by CellTypist.\nCellTypist requires data to be log-normalized\
|
||||
\ to 10000 counts per cell.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--var_reference_gene_names"
|
||||
description: "The name of the adata var column in the reference data containing\
|
||||
\ gene names; when no gene_name_layer is provided, the var index will be used.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Model arguments"
|
||||
description: "Model arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--model"
|
||||
description: "Pretrained model in pkl format. If not provided, the model will\
|
||||
\ be trained on the reference data and --reference should be provided."
|
||||
info: null
|
||||
example:
|
||||
- "pretrained_model.pkl"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--feature_selection"
|
||||
description: "Whether to perform feature selection."
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--majority_voting"
|
||||
description: "Whether to refine the predicted labels by running the majority voting\
|
||||
\ classifier after over-clustering."
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--C"
|
||||
description: "Inverse of regularization strength in logistic regression."
|
||||
info: null
|
||||
default:
|
||||
- 1.0
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--max_iter"
|
||||
description: "Maximum number of iterations before reaching the minimum of the\
|
||||
\ cost function."
|
||||
info: null
|
||||
default:
|
||||
- 1000
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--use_SGD"
|
||||
description: "Whether to use the stochastic gradient descent algorithm."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "double"
|
||||
name: "--min_prop"
|
||||
description: "\"For the dominant cell type within a subcluster, the minimum proportion\
|
||||
\ of cells required to \nsupport naming of the subcluster by this cell type.\
|
||||
\ Ignored if majority_voting is set to False. \nSubcluster that fails to pass\
|
||||
\ this proportion threshold will be assigned 'Heterogeneous'.\"\n"
|
||||
info: null
|
||||
default:
|
||||
- 0.0
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Output arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_predictions"
|
||||
description: "In which `.obs` slots to store the predicted information.\n"
|
||||
info: null
|
||||
default:
|
||||
- "celltypist_pred"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_probability"
|
||||
description: "In which `.obs` slots to store the probability of the predictions.\n"
|
||||
info: null
|
||||
default:
|
||||
- "celltypist_probability"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Automated cell type annotation tool for scRNA-seq datasets on the basis\
|
||||
\ of logistic regression classifiers optimised by the stochastic gradient descent\
|
||||
\ algorithm."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "annotation_test_data"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "libhdf5-dev"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scanpy~=1.9.6"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "celltypist==1.6.3"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/annotate/celltypist/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/annotate/celltypist"
|
||||
executable: "target/executable/annotate/celltypist/celltypist"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,367 +0,0 @@
|
||||
name: "onclass"
|
||||
namespace: "annotate"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Jakub Majercik"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "jakub@data-intuitive.com"
|
||||
github: "jakubmajercik"
|
||||
linkedin: "jakubmajercik"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatics Engineer"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Input dataset (query) arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "The input (query) data to be labeled. Should be a .h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_layer"
|
||||
description: "The layer in the input data to be used for cell type annotation\
|
||||
\ if .X is not to be used."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--cl_nlp_emb_file"
|
||||
description: "The .nlp.emb file with the cell type embeddings."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--cl_ontology_file"
|
||||
description: "The .ontology file with the cell type ontology."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--cl_obo_file"
|
||||
description: "The .obo file with the cell type ontology."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--var_query_gene_names"
|
||||
description: "The name of the adata var column in the input data containing gene\
|
||||
\ names; when no gene_name_layer is provided, the var index will be used.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Reference"
|
||||
description: "Arguments related to the reference dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--reference"
|
||||
description: "The reference data to train the CellTypist classifiers on. Only\
|
||||
\ required if a pre-trained --model is not provided."
|
||||
info: null
|
||||
example:
|
||||
- "reference.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_layer"
|
||||
description: "The layer in the reference data to be used for cell type annotation\
|
||||
\ if .X is not to be used."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_target"
|
||||
description: "The name of the adata obs column in the reference data containing\
|
||||
\ cell type annotations."
|
||||
info: null
|
||||
example:
|
||||
- "cell_ontology_class"
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Output arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_predictions"
|
||||
description: "In which `.obs` slots to store the predicted information.\n"
|
||||
info: null
|
||||
default:
|
||||
- "onclass_pred"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_probability"
|
||||
description: "In which `.obs` slots to store the probability of the predictions.\n"
|
||||
info: null
|
||||
default:
|
||||
- "onclass_prob"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Model arguments"
|
||||
description: "Model arguments"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--model"
|
||||
description: "\"Pretrained model path without a file extension. If not provided,\
|
||||
\ the model will be trained \non the reference data and --reference should be\
|
||||
\ provided. The path namespace should contain:\n - a .npz or .pkl file\n -\
|
||||
\ a .data file\n - a .meta file\n - a .index file\ne.g. /path/to/model/pretrained_model_target1\
|
||||
\ as saved by OnClass.\"\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--max_iter"
|
||||
description: "Maximum number of iterations for training the model."
|
||||
info: null
|
||||
default:
|
||||
- 30
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "OnClass is a python package for single-cell cell type annotation. It\
|
||||
\ uses the Cell Ontology to capture the cell type similarity. \nThese similarities\
|
||||
\ enable OnClass to annotate cell types that are never seen in the training data.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "annotation_test_data"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.8"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scikit-learn==0.24.0"
|
||||
- "OnClass==1.2"
|
||||
- "tensorflow==2.13.1"
|
||||
- "obonet==1.1.0"
|
||||
- "mudata"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/annotate/onclass/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/annotate/onclass"
|
||||
executable: "target/executable/annotate/onclass/onclass"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,387 +0,0 @@
|
||||
name: "popv"
|
||||
namespace: "annotate"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Matthias Beyens"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
github: "MatthiasBeyens"
|
||||
orcid: "0000-0003-3304-0706"
|
||||
email: "matthias.beyens@gmail.com"
|
||||
linkedin: "mbeyens"
|
||||
organizations:
|
||||
- name: "Janssen Pharmaceuticals"
|
||||
href: "https://www.janssen.com"
|
||||
role: "Principal Scientist"
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Arguments related to the input (aka query) dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_layer"
|
||||
description: "Which layer to use. If no value is provided, the counts are assumed\
|
||||
\ to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[input_layer]`."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_obs_batch"
|
||||
description: "Key in obs field of input adata for batch information. If no value\
|
||||
\ is provided, batch label is assumed to be unknown."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_var_subset"
|
||||
description: "Subset the input object with this column."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_obs_label"
|
||||
description: "Key in obs field of input adata for label information. This is only\
|
||||
\ used for training scANVI. Unlabelled cells should be set to `\"unknown_celltype_label\"\
|
||||
`."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--unknown_celltype_label"
|
||||
description: "If `input_obs_label` is specified, cells with this value will be\
|
||||
\ treated as unknown and will be predicted by the model."
|
||||
info: null
|
||||
default:
|
||||
- "unknown"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Reference"
|
||||
description: "Arguments related to the reference dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--reference"
|
||||
description: "User-provided reference tissue. The data that will be used as reference\
|
||||
\ to call cell types."
|
||||
info: null
|
||||
example:
|
||||
- "TS_Bladder_filtered.h5ad"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_layer"
|
||||
description: "Which layer to use. If no value is provided, the counts are assumed\
|
||||
\ to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[reference_layer]`."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_label"
|
||||
description: "Key in obs field of reference AnnData with cell-type information."
|
||||
info: null
|
||||
default:
|
||||
- "cell_ontology_class"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_batch"
|
||||
description: "Key in obs field of input adata for batch information."
|
||||
info: null
|
||||
default:
|
||||
- "donor_assay"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Output arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Arguments"
|
||||
description: "Other arguments."
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--methods"
|
||||
description: "Methods to call cell types. By default, runs to knn_on_scvi and\
|
||||
\ scanvi."
|
||||
info: null
|
||||
example:
|
||||
- "knn_on_scvi"
|
||||
- "scanvi"
|
||||
required: true
|
||||
choices:
|
||||
- "celltypist"
|
||||
- "knn_on_bbknn"
|
||||
- "knn_on_scanorama"
|
||||
- "knn_on_scvi"
|
||||
- "onclass"
|
||||
- "rf"
|
||||
- "scanvi"
|
||||
- "svm"
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Performs popular major vote cell typing on single cell sequence data\
|
||||
\ using multiple algorithms. Note that this is a one-shot version of PopV."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "annotation_test_data"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "highmem"
|
||||
- "highcpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.9-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
- "git"
|
||||
- "build-essential"
|
||||
- "wget"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scanpy~=1.9.6"
|
||||
- "scvi-tools~=1.0.3"
|
||||
- "popv~=0.3.2"
|
||||
- "jax==0.4.10"
|
||||
- "jaxlib==0.4.10"
|
||||
- "ml-dtypes<0.3.0"
|
||||
- "scipy==1.12.0"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
- type: "docker"
|
||||
run:
|
||||
- "cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \\\n\
|
||||
\ cd PopV && git fetch --depth 1 origin tag v0.2 && git checkout v0.2\n"
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/annotate/popv/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/annotate/popv"
|
||||
executable: "target/executable/annotate/popv/popv"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,388 +0,0 @@
|
||||
name: "random_forest_annotation"
|
||||
namespace: "annotate"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Jakub Majercik"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "jakub@data-intuitive.com"
|
||||
github: "jakubmajercik"
|
||||
linkedin: "jakubmajercik"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatics Engineer"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Input dataset (query) arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "The input (query) data to be labeled. Should be a .h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_layer"
|
||||
description: "The layer in the input data to be used for cell type annotation\
|
||||
\ if .X is not to be used."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Reference"
|
||||
description: "Arguments related to the reference dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--reference"
|
||||
description: "The reference data to train the CellTypist classifiers on. Only\
|
||||
\ required if a pre-trained --model is not provided."
|
||||
info: null
|
||||
example:
|
||||
- "reference.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_layer"
|
||||
description: "The layer in the reference data to be used for cell type annotation\
|
||||
\ if .X is not to be used. Data are expected to be processed in the same way\
|
||||
\ as the --input query dataset."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_target"
|
||||
description: "Key in obs field of reference modality with cell-type information."
|
||||
info: null
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Output arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_predictions"
|
||||
description: "In which `.obs` slots to store the predicted information.\n"
|
||||
info: null
|
||||
default:
|
||||
- "random_forest_pred"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_probability"
|
||||
description: "In which `.obs` slots to store the probability of the predictions.\n"
|
||||
info: null
|
||||
default:
|
||||
- "random_forest_probability"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Model arguments"
|
||||
description: "Model arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--model"
|
||||
description: "Pretrained model in pkl format. If not provided, the model will\
|
||||
\ be trained on the reference data and --reference should be provided."
|
||||
info: null
|
||||
example:
|
||||
- "pretrained_model.pkl"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--n_estimators"
|
||||
description: "Number of trees in the random forest."
|
||||
info: null
|
||||
default:
|
||||
- 100
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--max_depth"
|
||||
description: "Maximum depth of the trees in the random forest. \nIf not provided,\
|
||||
\ the nodes are expanded until all leaves only contain a single sample.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--criterion"
|
||||
description: "The function to measure the quality of a split."
|
||||
info: null
|
||||
default:
|
||||
- "gini"
|
||||
required: false
|
||||
choices:
|
||||
- "gini"
|
||||
- "entropy"
|
||||
- "log_loss"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--class_weight"
|
||||
description: "Weights associated with classes.\nThe `balanced` mode uses the values\
|
||||
\ of y to automatically adjust weights inversely proportional to class frequencies\
|
||||
\ in the input data.\nThe `balanced_subsample` mode is the same as `balanced`\
|
||||
\ except that weights are computed based on the bootstrap sample for every tree\
|
||||
\ grown.\nThe `uniform` mode gives all classes a weight of one.\n"
|
||||
info: null
|
||||
default:
|
||||
- "balanced_subsample"
|
||||
required: false
|
||||
choices:
|
||||
- "balanced"
|
||||
- "balanced_subsample"
|
||||
- "uniform"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--max_features"
|
||||
description: "The number of features to consider when looking for the best split.\
|
||||
\ The value can either be a positive integer or one of `sqrt`, `log2` or `all`.\n\
|
||||
If integer: consider max_features features at each split.\nIf `sqrt`: max_features\
|
||||
\ is the squareroot of all input features.\nIf `log2`: max_features is the log2\
|
||||
\ of all input features.\nIf `all`: max features equals all input features.\n"
|
||||
info: null
|
||||
default:
|
||||
- "200"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Automated cell type annotation tool for scRNA-seq datasets on the basis\
|
||||
\ of random forest."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "TS_Blood_filtered.h5mu"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.12-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "libhdf5-dev"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scikit-learn==1.4.2"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/annotate/random_forest_annotation/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/annotate/random_forest_annotation"
|
||||
executable: "target/executable/annotate/random_forest_annotation/random_forest_annotation"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,522 +0,0 @@
|
||||
name: "scanvi"
|
||||
namespace: "annotate"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Jakub Majercik"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "jakub@data-intuitive.com"
|
||||
github: "jakubmajercik"
|
||||
linkedin: "jakubmajercik"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatics Engineer"
|
||||
- name: "Weiwei Schultz"
|
||||
roles:
|
||||
- "contributor"
|
||||
info:
|
||||
role: "Contributor"
|
||||
organizations:
|
||||
- name: "Janssen R&D US"
|
||||
role: "Associate Director Data Sciences"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Arguments related to the input (aka query) dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Reference"
|
||||
description: "Arguments related to the reference dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--reference"
|
||||
description: "Reference h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "reference.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--scvi_reference_model"
|
||||
description: "Pretrained scvi reference model"
|
||||
info: null
|
||||
example:
|
||||
- "scvi_model.pt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_label"
|
||||
description: "Key in obs field of reference AnnData with cell-type information."
|
||||
info: null
|
||||
example:
|
||||
- "cell_ontology_class"
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "SCANVI reference model training arguments"
|
||||
description: "Arguments related to the reference SCANVI model."
|
||||
arguments:
|
||||
- type: "double"
|
||||
name: "--reference_train_size"
|
||||
description: "Size of training set."
|
||||
info: null
|
||||
default:
|
||||
- 0.9
|
||||
required: false
|
||||
min: 0.0
|
||||
max: 1.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--reference_max_epochs"
|
||||
description: "Maximum number of epochs."
|
||||
info: null
|
||||
default:
|
||||
- 400
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--reference_learning_rate"
|
||||
description: "Learning rate."
|
||||
info: null
|
||||
default:
|
||||
- 0.001
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--reference_reduce_lr_on_plateau"
|
||||
description: "Reduce learning rate on plateau."
|
||||
info: null
|
||||
default:
|
||||
- true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--reference_lr_patience"
|
||||
description: "Patience for learning rate reduction."
|
||||
info: null
|
||||
default:
|
||||
- 25
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--reference_lr_factor"
|
||||
description: "Factor by which to reduce learning rate."
|
||||
info: null
|
||||
default:
|
||||
- 0.5
|
||||
required: false
|
||||
min: 0.0
|
||||
max: 1.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--reference_early_stopping"
|
||||
description: "Early stopping."
|
||||
info: null
|
||||
default:
|
||||
- true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--reference_early_stopping_patience"
|
||||
description: "Patience for early stopping."
|
||||
info: null
|
||||
default:
|
||||
- 50
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "SCANVI query model training arguments"
|
||||
description: "Arguments related to the query SCANVI model."
|
||||
arguments:
|
||||
- type: "double"
|
||||
name: "--query_train_size"
|
||||
description: "Size of training set."
|
||||
info: null
|
||||
default:
|
||||
- 0.9
|
||||
required: false
|
||||
min: 0.0
|
||||
max: 1.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--query_max_epochs"
|
||||
description: "Maximum number of epochs."
|
||||
info: null
|
||||
default:
|
||||
- 400
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--query_learning_rate"
|
||||
description: "Learning rate."
|
||||
info: null
|
||||
default:
|
||||
- 0.001
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--query_reduce_lr_on_plateau"
|
||||
description: "Reduce learning rate on plateau."
|
||||
info: null
|
||||
default:
|
||||
- true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--query_lr_patience"
|
||||
description: "Patience for learning rate reduction."
|
||||
info: null
|
||||
default:
|
||||
- 25
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--query_lr_factor"
|
||||
description: "Factor by which to reduce learning rate."
|
||||
info: null
|
||||
default:
|
||||
- 0.5
|
||||
required: false
|
||||
min: 0.0
|
||||
max: 1.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--query_early_stopping"
|
||||
description: "Early stopping."
|
||||
info: null
|
||||
default:
|
||||
- true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--query_early_stopping_patience"
|
||||
description: "Patience for early stopping."
|
||||
info: null
|
||||
default:
|
||||
- 50
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Arguments related to the output."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_model"
|
||||
description: "Folder where the state of the trained model will be saved to."
|
||||
info: null
|
||||
example:
|
||||
- "model_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_predictions"
|
||||
description: "In which `.obs` slots to store the predicted information.\n"
|
||||
info: null
|
||||
default:
|
||||
- "scanvi_pred"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_probability"
|
||||
description: "In which `.obs` slots to store the probability of the predictions.\n"
|
||||
info: null
|
||||
default:
|
||||
- "scanvi_probability"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obsm_scanvi_embedding"
|
||||
description: "In which `.obsm` slots to store the scvi embedding.\n"
|
||||
info: null
|
||||
default:
|
||||
- "scanvi_embedding"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--unknown_celltype"
|
||||
description: "Label for unknown cell types.\n"
|
||||
info: null
|
||||
default:
|
||||
- "Unknown"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Semi-supervised model for single-cell transcriptomics data. A scVI extension\
|
||||
\ that can leverage the cell type knowledge for a subset of the cells present in\
|
||||
\ the data sets to infer the states of the rest of the cells."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "annotation_test_data"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.12-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scanpy~=1.9.6"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scvi-tools==1.1.5"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/annotate/scanvi/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/annotate/scanvi"
|
||||
executable: "target/executable/annotate/scanvi/scanvi"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,370 +0,0 @@
|
||||
name: "svm_annotation"
|
||||
namespace: "annotate"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Jakub Majercik"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "jakub@data-intuitive.com"
|
||||
github: "jakubmajercik"
|
||||
linkedin: "jakubmajercik"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatics Engineer"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Input dataset (query) arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "The input (query) data to be labeled. Should be a .h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_layer"
|
||||
description: "The layer in the input data to be used for cell type annotation\
|
||||
\ if .X is not to be used."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Reference"
|
||||
description: "Arguments related to the reference dataset."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--reference"
|
||||
description: "The reference data to train the CellTypist classifiers on. Only\
|
||||
\ required if a pre-trained --model is not provided."
|
||||
info: null
|
||||
example:
|
||||
- "reference.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_layer"
|
||||
description: "The layer in the reference data to be used for cell type annotation\
|
||||
\ if .X is not to be used. Data are expected to be processed in the same way\
|
||||
\ as the --input query dataset."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--reference_obs_target"
|
||||
info: null
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Output arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_prediction"
|
||||
description: "In which `.obs` slots to store the predicted information.\n"
|
||||
info: null
|
||||
default:
|
||||
- "svm_pred"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_obs_probability"
|
||||
description: "In which `.obs` slots to store the probability of the predictions.\n"
|
||||
info: null
|
||||
default:
|
||||
- "svm_probability"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Model arguments"
|
||||
description: "Model arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--model"
|
||||
description: "Pretrained model in pkl format. If not provided, the model will\
|
||||
\ be trained on the reference data and --reference should be provided."
|
||||
info: null
|
||||
example:
|
||||
- "pretrained_model.pkl"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--feature_selection"
|
||||
description: "Whether to perform feature selection."
|
||||
info: null
|
||||
default:
|
||||
- true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--max_iter"
|
||||
description: "Maximum number of iterations for the SVM."
|
||||
info: null
|
||||
default:
|
||||
- 5000
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--c_reg"
|
||||
description: "Regularization parameter for the SVM."
|
||||
info: null
|
||||
default:
|
||||
- 1.0
|
||||
required: false
|
||||
min: 0.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--class_weight"
|
||||
description: "\"Class weights for the SVM. The `uniform` mode gives all classes\
|
||||
\ a weight of one. \nThe `balanced` mode (default) uses the values of y to\
|
||||
\ automatically adjust weights inversely \nproportional to class frequencies\
|
||||
\ in the input data as n_samples / (n_classes * np.bincount(y))\"\n"
|
||||
info: null
|
||||
default:
|
||||
- "balanced"
|
||||
required: false
|
||||
choices:
|
||||
- "balanced"
|
||||
- "uniform"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Automated cell type annotation tool for scRNA-seq datasets on the basis\
|
||||
\ of SVMs."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "annotation_test_data"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.12-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "libhdf5-dev"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scikit-learn==1.5.2"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/annotate/svm_annotation/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/annotate/svm_annotation"
|
||||
executable: "target/executable/annotate/svm_annotation/svm_annotation"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,281 +0,0 @@
|
||||
name: "leiden"
|
||||
namespace: "cluster"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries De Maeyer"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "ddemaeyer@gmail.com"
|
||||
github: "ddemaeyer"
|
||||
linkedin: "dries-de-maeyer-b46a814"
|
||||
organizations:
|
||||
- name: "Janssen Pharmaceuticals"
|
||||
href: "https://www.janssen.com"
|
||||
role: "Principal Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsp_connectivities"
|
||||
description: "In which .obsp slot the neighbor connectivities can be found."
|
||||
info: null
|
||||
default:
|
||||
- "connectivities"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsm_name"
|
||||
description: "Name of the .obsm key under which to add the cluster labels.\nThe\
|
||||
\ name of the columns in the matrix will correspond to the resolutions.\n"
|
||||
info: null
|
||||
default:
|
||||
- "leiden"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--resolution"
|
||||
description: "A parameter value controlling the coarseness of the clustering.\
|
||||
\ Higher values lead to more clusters.\nMultiple values will result in clustering\
|
||||
\ being performed multiple times.\n"
|
||||
info: null
|
||||
default:
|
||||
- 1.0
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Cluster cells using the [Leiden algorithm] [Traag18] implemented in\
|
||||
\ the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain\
|
||||
\ algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15]\
|
||||
\ [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn`\
|
||||
\ first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in\
|
||||
\ large networks, J. Stat. Mech. \n[Levine15]: Levine et al. (2015), Data-Driven\
|
||||
\ Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with\
|
||||
\ Prognosis, Cell. \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing\
|
||||
\ well-connected communities arXiv. \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale\
|
||||
\ single-cell gene expression data analysis, Genome Biology. \n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "highcpu"
|
||||
- "midmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
- "leidenalg~=0.10.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/cluster/leiden/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/cluster/leiden"
|
||||
executable: "target/executable/cluster/leiden/leiden"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,226 +0,0 @@
|
||||
name: "compress_h5mu"
|
||||
namespace: "compression"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Path to the input .h5mu."
|
||||
info: null
|
||||
example:
|
||||
- "sample_path"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "location of output file."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--compression"
|
||||
description: "Compression type."
|
||||
info: null
|
||||
default:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "lzf"
|
||||
- "gzip"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "compress_h5mu.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Compress a MuData file. \n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "run_test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "singlecpu"
|
||||
- "lowmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/compression/compress_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/compression/compress_h5mu"
|
||||
executable: "target/executable/compression/compress_h5mu/compress_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,49 +0,0 @@
|
||||
from h5py import File as H5File
|
||||
from h5py import Group, Dataset
|
||||
from pathlib import Path
|
||||
from typing import Union, Literal
|
||||
from functools import partial
|
||||
|
||||
|
||||
def compress_h5mu(input_path: Union[str, Path],
|
||||
output_path: Union[str, Path],
|
||||
compression: Union[Literal['gzip'], Literal['lzf']]):
|
||||
input_path, output_path = str(input_path), str(output_path)
|
||||
|
||||
def copy_attributes(in_object, out_object):
|
||||
for key, value in in_object.attrs.items():
|
||||
out_object.attrs[key] = value
|
||||
|
||||
def visit_path(output_h5: H5File,
|
||||
compression: Union[Literal['gzip'], Literal['lzf']],
|
||||
name: str, object: Union[Group, Dataset]):
|
||||
if isinstance(object, Group):
|
||||
new_group = output_h5.create_group(name)
|
||||
copy_attributes(object, new_group)
|
||||
elif isinstance(object, Dataset):
|
||||
# Compression only works for non-scalar Dataset objects
|
||||
# Scalar objects dont have a shape defined
|
||||
if not object.compression and object.shape not in [None, ()]:
|
||||
new_dataset = output_h5.create_dataset(name, data=object, compression=compression)
|
||||
copy_attributes(object, new_dataset)
|
||||
else:
|
||||
output_h5.copy(object, name)
|
||||
else:
|
||||
raise NotImplementedError(f"Could not copy element {name}, "
|
||||
f"type has not been implemented yet: {type(object)}")
|
||||
|
||||
with H5File(input_path, 'r') as input_h5, H5File(output_path, 'w', userblock_size=512) as output_h5:
|
||||
copy_attributes(input_h5, output_h5)
|
||||
input_h5.visititems(partial(visit_path, output_h5, compression))
|
||||
|
||||
with open(input_path, "rb") as input_bytes:
|
||||
# Mudata puts metadata like this in the first 512 bytes:
|
||||
# MuData (format-version=0.1.0;creator=muon;creator-version=0.2.0)
|
||||
# See mudata/_core/io.py, read_h5mu() function
|
||||
starting_metadata = input_bytes.read(100)
|
||||
# The metadata is padded with extra null bytes up until 512 bytes
|
||||
truncate_location = starting_metadata.find(b"\x00")
|
||||
starting_metadata = starting_metadata[:truncate_location]
|
||||
with open(output_path, "br+") as f:
|
||||
nbytes = f.write(starting_metadata)
|
||||
f.write(b"\0" * (512 - nbytes))
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,200 +0,0 @@
|
||||
name: "tar_extract"
|
||||
namespace: "compression"
|
||||
version: "dev"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input file"
|
||||
info: null
|
||||
example:
|
||||
- "input.tar.gz"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Folder to restore file(s) to."
|
||||
info: null
|
||||
example:
|
||||
- "output_folder"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--strip_components"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Strip this amount of leading components from file names on extraction.\
|
||||
\ For example, to extract only 'myfile.txt' from an archive containing the structure\
|
||||
\ `this/goes/deep/myfile.txt', use 3 to strip 'this/goes/deep/'."
|
||||
info: null
|
||||
example:
|
||||
- 1
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--exclude"
|
||||
alternatives:
|
||||
- "-e"
|
||||
description: "Prevents any file or member whose name matches the shell wildcard\
|
||||
\ (pattern) from being extracted."
|
||||
info: null
|
||||
example:
|
||||
- "docs/figures"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Extract files from a tar archive"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "LICENSE"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "singlecpu"
|
||||
- "lowmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:latest"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/compression/tar_extract/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/compression/tar_extract"
|
||||
executable: "target/executable/compression/tar_extract/tar_extract"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,332 +0,0 @@
|
||||
name: "from_10xh5_to_h5mu"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "A 10x h5 file as generated by Cell Ranger."
|
||||
info: null
|
||||
example:
|
||||
- "raw_feature_bc_matrix.h5"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input_metrics_summary"
|
||||
description: "A metrics summary csv file as generated by Cell Ranger."
|
||||
info: null
|
||||
example:
|
||||
- "metrics_cellranger.h5"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output h5mu file."
|
||||
info:
|
||||
slots:
|
||||
mod:
|
||||
- name: "rna"
|
||||
required: true
|
||||
description: "Gene expression counts."
|
||||
slots:
|
||||
var:
|
||||
- name: "gene_symbol"
|
||||
type: "string"
|
||||
description: "Identification of the gene."
|
||||
required: true
|
||||
- name: "feature_types"
|
||||
type: "string"
|
||||
description: "The full name of the modality."
|
||||
required: true
|
||||
- name: "genome"
|
||||
type: "string"
|
||||
description: "Reference that was used to generate the data."
|
||||
required: true
|
||||
- name: "prot"
|
||||
required: false
|
||||
description: "Protein abundancy"
|
||||
slots:
|
||||
var:
|
||||
- name: "gene_symbol"
|
||||
type: "string"
|
||||
description: "Identification of the gene."
|
||||
required: true
|
||||
- name: "feature_types"
|
||||
type: "string"
|
||||
description: "The full name of the modality."
|
||||
required: true
|
||||
- name: "genome"
|
||||
type: "string"
|
||||
description: "Reference that was used to generate the data."
|
||||
required: true
|
||||
- name: "vdj"
|
||||
required: false
|
||||
description: "VDJ transcript counts"
|
||||
slots:
|
||||
var:
|
||||
- name: "gene_symbol"
|
||||
type: "string"
|
||||
description: "Identification of the gene."
|
||||
required: true
|
||||
- name: "feature_types"
|
||||
type: "string"
|
||||
description: "The full name of the modality."
|
||||
required: true
|
||||
- name: "genome"
|
||||
type: "string"
|
||||
description: "Reference that was used to generate the data."
|
||||
required: true
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--uns_metrics"
|
||||
description: "Name of the .uns slot under which to QC metrics (if any)."
|
||||
info: null
|
||||
default:
|
||||
- "metrics_cellranger"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "integer"
|
||||
name: "--min_genes"
|
||||
description: "Minimum number of counts required for a cell to pass filtering."
|
||||
info: null
|
||||
example:
|
||||
- 100
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_counts"
|
||||
description: "Minimum number of genes expressed required for a cell to pass filtering."
|
||||
info: null
|
||||
example:
|
||||
- 1000
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Converts a 10x h5 into an h5mu file.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.9-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_10xh5_to_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_10xh5_to_h5mu"
|
||||
executable: "target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,233 +0,0 @@
|
||||
name: "from_10xmtx_to_h5mu"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input mtx folder"
|
||||
info: null
|
||||
example:
|
||||
- "input_dir_containing_gz_files"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Converts a 10x mtx into an h5mu file.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "run_test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_10xmtx_to_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_10xmtx_to_h5mu"
|
||||
executable: "target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,209 +0,0 @@
|
||||
name: "from_bd_to_10x_molecular_barcode_tags"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input SAM or BAM file."
|
||||
info: null
|
||||
example:
|
||||
- "input.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output alignment file."
|
||||
info: null
|
||||
example:
|
||||
- "output.sam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--bam"
|
||||
description: "Output a BAM file."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--threads"
|
||||
alternatives:
|
||||
- "-t"
|
||||
description: "Number of threads"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Convert the molecular barcode sequence SAM tag from BD format (MA) to\
|
||||
\ 10X format (UB).\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "run_test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "output_raw"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:latest"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "samtools"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_bd_to_10x_molecular_barcode_tags"
|
||||
executable: "target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,242 +0,0 @@
|
||||
name: "from_bdrhap_to_h5mu"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dorien Roosen"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dorien@data-intuitive.com"
|
||||
github: "dorien-er"
|
||||
linkedin: "dorien-roosen"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--id"
|
||||
description: "A sample ID."
|
||||
info: null
|
||||
example:
|
||||
- "my_id"
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "The output h5mu of a BD Rhapsody workflow."
|
||||
info: null
|
||||
example:
|
||||
- "sample.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "sample.h5mu"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_bdrhap_to_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_bdrhap_to_h5mu"
|
||||
executable: "target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,259 +0,0 @@
|
||||
name: "from_cellranger_multi_to_h5mu"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input folder. Must contain the output from a cellranger multi run."
|
||||
info: null
|
||||
example:
|
||||
- "input_dir_containing_modalities"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Locations for the output files. Must contain a wildcard (*) character,\n\
|
||||
which will be replaced with the sample name.\n"
|
||||
info: null
|
||||
example:
|
||||
- "*.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_csv"
|
||||
description: "CSV file describing the sample name per output file"
|
||||
info: null
|
||||
example:
|
||||
- "samples.csv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--uns_metrics"
|
||||
description: "Name of the .uns slot under which to QC metrics (if any)."
|
||||
info: null
|
||||
default:
|
||||
- "metrics_cellranger"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Converts the output from cellranger multi to a single .h5mu file.\n\
|
||||
By default, will map the following library type names to modality names:\n - Gene\
|
||||
\ Expression: rna\n - Peaks: atac\n - Antibody Capture: prot\n - VDJ: vdj\n \
|
||||
\ - VDJ-T: vdj_t\n - VDJ-B: vdj_b\n - CRISPR Guide Capture: crispr\n - Multiplexing\
|
||||
\ Capture: hashing\n \nOther library types have their whitepace removed and dashes\
|
||||
\ replaced by\nunderscores to generate the modality name.\n\nCurrently does not\
|
||||
\ allow parsing the output from cell barcode demultiplexing.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "10x_5k_anticmv"
|
||||
- type: "file"
|
||||
path: "10x_5k_lung_crispr"
|
||||
- type: "file"
|
||||
path: "10x_5k_beam"
|
||||
- type: "file"
|
||||
path: "10x_5k_fixed"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
- "scirpy~=0.12.0"
|
||||
- "pandas~=2.2.2"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_cellranger_multi_to_h5mu"
|
||||
executable: "target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,237 +0,0 @@
|
||||
name: "from_h5ad_to_h5mu"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries De Maeyer"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "ddemaeyer@gmail.com"
|
||||
github: "ddemaeyer"
|
||||
linkedin: "dries-de-maeyer-b46a814"
|
||||
organizations:
|
||||
- name: "Janssen Pharmaceuticals"
|
||||
href: "https://www.janssen.com"
|
||||
role: "Principal Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input h5ad files"
|
||||
info: null
|
||||
default:
|
||||
- "input.h5ad"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output MuData file."
|
||||
info: null
|
||||
default:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Converts a single layer h5ad file into a single MuData object\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.9-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_h5ad_to_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_h5ad_to_h5mu"
|
||||
executable: "target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,242 +0,0 @@
|
||||
name: "from_h5mu_to_h5ad"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input MuData file"
|
||||
info: null
|
||||
default:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output AnnData file."
|
||||
info: null
|
||||
default:
|
||||
- "output.h5ad"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the final h5ad object."
|
||||
info: null
|
||||
default:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Converts a h5mu file into a h5ad file.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.9-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_h5mu_to_h5ad/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_h5mu_to_h5ad"
|
||||
executable: "target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,216 +0,0 @@
|
||||
name: "from_h5mu_to_seurat"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input h5mu file"
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output Seurat file"
|
||||
info: null
|
||||
example:
|
||||
- "output.rds"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "r_script"
|
||||
path: "script.R"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Converts an h5mu file into a Seurat file.\n\nRestrictions:\n - Only\
|
||||
\ the intersection of cells is currently loaded into the Seurat object due to the\
|
||||
\ object structure limitation.\n - Multimodal embeddings (global .obsm slot) are\
|
||||
\ loaded with the assay.used field set to the default assay.\n - Embeddings names\
|
||||
\ are changed in order to comply with R & Seurat requirements and conventions.\n\
|
||||
\ - Feature names with underscores ('_') are automatically replaced with dashes\
|
||||
\ ('-')\n - Seurat does not support global variables metadata /var.\n"
|
||||
test_resources:
|
||||
- type: "r_script"
|
||||
path: "run_test.R"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "10x_5k_anticmv"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "singlecpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "rocker/r2u:24.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "libhdf5-dev"
|
||||
- "libgeos-dev"
|
||||
interactive: false
|
||||
- type: "r"
|
||||
cran:
|
||||
- "anndata"
|
||||
- "hdf5r"
|
||||
- "testthat"
|
||||
- "SeuratObject"
|
||||
- "Seurat"
|
||||
bioc_force_install: false
|
||||
- type: "r"
|
||||
github:
|
||||
- "pmbio/MuDataSeurat@empty-tables-and-nullable"
|
||||
bioc_force_install: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/convert/from_h5mu_to_seurat/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/from_h5mu_to_seurat"
|
||||
executable: "target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,301 +0,0 @@
|
||||
name: "velocyto_to_h5mu"
|
||||
namespace: "convert"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
- "author"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
- name: "Angela Oliveira Pisco"
|
||||
roles:
|
||||
- "contributor"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
github: "aopisco"
|
||||
orcid: "0000-0003-0142-2355"
|
||||
linkedin: "aopisco"
|
||||
organizations:
|
||||
- name: "Insitro"
|
||||
href: "https://insitro.com"
|
||||
role: "Director of Computational Biology"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input_loom"
|
||||
description: "Path to the input loom file."
|
||||
info: null
|
||||
example:
|
||||
- "input.loom"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--input_h5mu"
|
||||
description: "If a MuData file is provided,"
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "The name of the modality to operate on."
|
||||
info: null
|
||||
default:
|
||||
- "rna_velocity"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Path to the output MuData file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--layer_spliced"
|
||||
description: "Output layer for the spliced reads."
|
||||
info: null
|
||||
default:
|
||||
- "velo_spliced"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--layer_unspliced"
|
||||
description: "Output layer for the unspliced reads."
|
||||
info: null
|
||||
default:
|
||||
- "velo_unspliced"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--layer_ambiguous"
|
||||
description: "Output layer for the ambiguous reads."
|
||||
info: null
|
||||
default:
|
||||
- "velo_ambiguous"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Convert a velocyto loom file to a h5mu file.\n\nIf an input h5mu file\
|
||||
\ is also provided, the velocity\nh5ad object will get added to that h5mu instead.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "cellranger_tiny_fastq"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowmem"
|
||||
- "lowcpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
- "loompy"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/velocity/velocyto_to_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/convert/velocyto_to_h5mu"
|
||||
executable: "target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,6 +1,6 @@
|
||||
name: "cellbender_remove_background"
|
||||
namespace: "correction"
|
||||
version: "dev"
|
||||
version: "fix-integration-tests"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
@@ -573,7 +573,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
target_tag: "fix-integration-tests"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
@@ -606,12 +606,12 @@ build_info:
|
||||
output: "target/executable/correction/cellbender_remove_background"
|
||||
executable: "target/executable/correction/cellbender_remove_background/cellbender_remove_background"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
git_commit: "c1fe2a629d77a3b17f3fb3f70217f017d8b2c549"
|
||||
git_remote: "https://x-access-token:ghs_goWtdwODyO3okSzUw3tKCvxN3t2lR82RHHnr@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1928-gc1fe2a62"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
version: "fix-integration-tests"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
@@ -624,10 +624,10 @@ package_config:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
# cellbender_remove_background dev
|
||||
# cellbender_remove_background fix-integration-tests
|
||||
#
|
||||
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
|
||||
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
|
||||
|
||||
# ViashHelp: Display helpful explanation about this executable
|
||||
function ViashHelp {
|
||||
echo "cellbender_remove_background dev"
|
||||
echo "cellbender_remove_background fix-integration-tests"
|
||||
echo ""
|
||||
echo "Eliminating technical artifacts from high-throughput single-cell RNA sequencing"
|
||||
echo "data."
|
||||
@@ -742,10 +742,10 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "lxml~=4.8.0" "mudata~=0.2.1" "cellbender~=0.3.0"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background"
|
||||
LABEL org.opencontainers.image.created="2024-10-17T17:49:04Z"
|
||||
LABEL org.opencontainers.image.created="2024-10-18T06:51:15Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
|
||||
LABEL org.opencontainers.image.revision="2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
LABEL org.opencontainers.image.version="dev"
|
||||
LABEL org.opencontainers.image.revision="c1fe2a629d77a3b17f3fb3f70217f017d8b2c549"
|
||||
LABEL org.opencontainers.image.version="fix-integration-tests"
|
||||
|
||||
VIASHDOCKER
|
||||
fi
|
||||
@@ -881,7 +881,7 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--version)
|
||||
echo "cellbender_remove_background dev"
|
||||
echo "cellbender_remove_background fix-integration-tests"
|
||||
exit
|
||||
;;
|
||||
--input)
|
||||
@@ -1452,7 +1452,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
|
||||
# determine docker image id
|
||||
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background:dev'
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background:fix-integration-tests'
|
||||
fi
|
||||
|
||||
# print dockerfile
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
name: "cellbender_remove_background_v0_2"
|
||||
namespace: "correction"
|
||||
version: "dev"
|
||||
version: "fix-integration-tests"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
arguments:
|
||||
@@ -372,7 +372,7 @@ engines:
|
||||
id: "docker"
|
||||
image: "nvcr.io/nvidia/pytorch:23.12-py3"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
target_tag: "fix-integration-tests"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "python"
|
||||
@@ -402,12 +402,12 @@ build_info:
|
||||
output: "target/executable/correction/cellbender_remove_background_v0_2"
|
||||
executable: "target/executable/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
git_commit: "c1fe2a629d77a3b17f3fb3f70217f017d8b2c549"
|
||||
git_remote: "https://x-access-token:ghs_goWtdwODyO3okSzUw3tKCvxN3t2lR82RHHnr@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1928-gc1fe2a62"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
version: "fix-integration-tests"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
@@ -420,10 +420,10 @@ package_config:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
#!/usr/bin/env bash
|
||||
|
||||
# cellbender_remove_background_v0_2 dev
|
||||
# cellbender_remove_background_v0_2 fix-integration-tests
|
||||
#
|
||||
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
|
||||
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
||||
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
|
||||
|
||||
# ViashHelp: Display helpful explanation about this executable
|
||||
function ViashHelp {
|
||||
echo "cellbender_remove_background_v0_2 dev"
|
||||
echo "cellbender_remove_background_v0_2 fix-integration-tests"
|
||||
echo ""
|
||||
echo "Eliminating technical artifacts from high-throughput single-cell RNA sequencing"
|
||||
echo "data."
|
||||
@@ -608,10 +608,10 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "anndata==0.10.8" "mudata~=0.2.4" "pandas!=2.1.2" "numpy<2.0.0" "muon==0.1.5" "cellbender==0.2.1"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background_v0_2"
|
||||
LABEL org.opencontainers.image.created="2024-10-17T17:49:04Z"
|
||||
LABEL org.opencontainers.image.created="2024-10-18T06:51:14Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
|
||||
LABEL org.opencontainers.image.revision="2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
LABEL org.opencontainers.image.version="dev"
|
||||
LABEL org.opencontainers.image.revision="c1fe2a629d77a3b17f3fb3f70217f017d8b2c549"
|
||||
LABEL org.opencontainers.image.version="fix-integration-tests"
|
||||
|
||||
VIASHDOCKER
|
||||
fi
|
||||
@@ -747,7 +747,7 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--version)
|
||||
echo "cellbender_remove_background_v0_2 dev"
|
||||
echo "cellbender_remove_background_v0_2 fix-integration-tests"
|
||||
exit
|
||||
;;
|
||||
--input)
|
||||
@@ -1114,7 +1114,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
|
||||
# determine docker image id
|
||||
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background_v0_2:dev'
|
||||
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background_v0_2:fix-integration-tests'
|
||||
fi
|
||||
|
||||
# print dockerfile
|
||||
|
||||
@@ -1,306 +0,0 @@
|
||||
name: "concatenate_h5mu"
|
||||
namespace: "dataflow"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Paths to the different samples to be concatenated."
|
||||
info: null
|
||||
example:
|
||||
- "sample_paths"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--input_id"
|
||||
description: "Names of the different samples that have to be concatenated. Must\
|
||||
\ be specified when using '--mode move'.\nIn this case, the ids will be used\
|
||||
\ for the columns names of the dataframes registring the conflicts.\nIf specified,\
|
||||
\ must be of same length as `--input`.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obs_sample_name"
|
||||
description: "Name of the .obs key under which to add the sample names."
|
||||
info: null
|
||||
default:
|
||||
- "sample_id"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--other_axis_mode"
|
||||
description: "How to handle the merging of other axis (var, obs, ...).\n\n -\
|
||||
\ None: keep no data\n - same: only keep elements of the matrices which are\
|
||||
\ the same in each of the samples\n - unique: only keep elements for which\
|
||||
\ there is only 1 possible value (1 value that can occur in multiple samples)\n\
|
||||
\ - first: keep the annotation from the first sample\n - only: keep elements\
|
||||
\ that show up in only one of the objects (1 unique element in only 1 sample)\n\
|
||||
\ - move: identical to 'same', but moving the conflicting values to .varm or\
|
||||
\ .obsm\n"
|
||||
info: null
|
||||
default:
|
||||
- "move"
|
||||
required: false
|
||||
choices:
|
||||
- "same"
|
||||
- "unique"
|
||||
- "first"
|
||||
- "only"
|
||||
- "concat"
|
||||
- "move"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--uns_merge_mode"
|
||||
description: "How to handle the merging of .uns across modalities\n - None: keep\
|
||||
\ no data\n - same: only keep elements of the matrices which are the same in\
|
||||
\ each of the samples\n - unique: only keep elements for which there is only\
|
||||
\ 1 possible value (1 value that can occur in multiple samples)\n - first:\
|
||||
\ keep the annotation from the first sample\n - only: keep elements that show\
|
||||
\ up in only one of the objects (1 unique element in only 1 sample)\n - make_unique:\
|
||||
\ identical to 'unique', but keys which are not unique are made unique by prefixing\
|
||||
\ them with the sample id.\n"
|
||||
info: null
|
||||
default:
|
||||
- "make_unique"
|
||||
required: false
|
||||
choices:
|
||||
- "same"
|
||||
- "unique"
|
||||
- "first"
|
||||
- "only"
|
||||
- "make_unique"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Concatenate observations from samples in several (uni- and/or multi-modal)\
|
||||
\ MuData files into a single file.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"
|
||||
- type: "file"
|
||||
path: "human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "midcpu"
|
||||
- "highmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "pandas~=2.1.1"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/concatenate_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/dataflow/concatenate_h5mu"
|
||||
executable: "target/executable/dataflow/concatenate_h5mu/concatenate_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,234 +0,0 @@
|
||||
name: "merge"
|
||||
namespace: "dataflow"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Paths to the single-modality .h5mu files that need to be combined"
|
||||
info: null
|
||||
default:
|
||||
- "sample_paths"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Path to the output file."
|
||||
info: null
|
||||
default:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Combine one or more single-modality .h5mu files together into one .h5mu\
|
||||
\ file.\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3_filtered_feature_bc_matrix_rna.h5mu"
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3_filtered_feature_bc_matrix_prot.h5mu"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "singlecpu"
|
||||
- "highmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "pandas~=2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/merge/config.vsh.yml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/dataflow/merge"
|
||||
executable: "target/executable/dataflow/merge/merge"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
@@ -1,268 +0,0 @@
|
||||
name: "split_h5mu"
|
||||
namespace: "dataflow"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dorien Roosen"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dorien@data-intuitive.com"
|
||||
github: "dorien-er"
|
||||
linkedin: "dorien-roosen"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Input & specifications"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Path to a single .h5mu file."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obs_feature"
|
||||
description: "The .obs column to split the mudata on."
|
||||
info: null
|
||||
example:
|
||||
- "celltype"
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--drop_obs_nan"
|
||||
description: "Whether to drop all .obs columns that contain only nan values after\
|
||||
\ splitting."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--ensure_unique_filenames"
|
||||
description: "Append number suffixes to ensure unique filenames after sanitizing\
|
||||
\ obs feature values."
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "Outputs"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "Output directory containing multiple h5mu files."
|
||||
info: null
|
||||
example:
|
||||
- "/path/to/output"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_files"
|
||||
description: "A csv containing the base filename and obs feature by which it was\
|
||||
\ split."
|
||||
info: null
|
||||
example:
|
||||
- "sample_files.csv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Split the samples of a single modality from a .h5mu (multimodal) sample\
|
||||
\ into seperate .h5mu files based on the values of an .obs column of this modality.\
|
||||
\ \n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "singlecpu"
|
||||
- "lowmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.12-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/split_h5mu/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/dataflow/split_h5mu"
|
||||
executable: "target/executable/dataflow/split_h5mu/split_h5mu"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,309 +0,0 @@
|
||||
name: "split_h5mu_train_test"
|
||||
namespace: "dataflow"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Jakub Majercik"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "jakub@data-intuitive.com"
|
||||
github: "jakubmajercik"
|
||||
linkedin: "jakubmajercik"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Bioinformatics Engineer"
|
||||
argument_groups:
|
||||
- name: "Inputs"
|
||||
description: "Input dataset in mudata format."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "The input (query) data to be labeled. Should be a .h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
description: "Which modality to process."
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Outputs"
|
||||
description: "Output arguments."
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_train"
|
||||
description: "The output training data in mudata format."
|
||||
info: null
|
||||
example:
|
||||
- "output_train.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_test"
|
||||
description: "The output testing data in mudata format."
|
||||
info: null
|
||||
example:
|
||||
- "output_test.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_val"
|
||||
description: "The output validation data in mudata format."
|
||||
info: null
|
||||
example:
|
||||
- "output_val.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--compression"
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Split arguments"
|
||||
description: "Model arguments."
|
||||
arguments:
|
||||
- type: "double"
|
||||
name: "--test_size"
|
||||
description: "The proportion of the dataset to include in the test split."
|
||||
info: null
|
||||
default:
|
||||
- 0.2
|
||||
required: false
|
||||
min: 0.0
|
||||
max: 1.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "double"
|
||||
name: "--val_size"
|
||||
description: "The proportion of the dataset to include in the validation split."
|
||||
info: null
|
||||
required: false
|
||||
min: 0.0
|
||||
max: 1.0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--shuffle"
|
||||
description: "Whether or not to shuffle the data before splitting."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--random_state"
|
||||
description: "The seed used by the random number generator."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Split mudata object into training and testing (and validation) datasets\
|
||||
\ based on observations into separate mudata objects."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3_mms.h5mu"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "libhdf5-dev"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scanpy~=1.9.6"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "scikit-learn==1.4.2"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/split_h5mu_train_test/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/dataflow/split_h5mu_train_test"
|
||||
executable: "target/executable/dataflow/split_h5mu_train_test/split_h5mu_train_test"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,259 +0,0 @@
|
||||
name: "split_modalities"
|
||||
namespace: "dataflow"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
||||
orcid: "0000-0002-4389-0440"
|
||||
linkedin: "dries-schaumont"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "contributor"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Path to a single .h5mu file."
|
||||
info: null
|
||||
default:
|
||||
- "sample_path"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output directory containing multiple h5mu files."
|
||||
info: null
|
||||
example:
|
||||
- "/path/to/output"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_types"
|
||||
description: "A csv containing the base filename and modality type per output\
|
||||
\ file."
|
||||
info: null
|
||||
example:
|
||||
- "types.csv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Split the modalities from a single .h5mu multimodal sample into seperate\
|
||||
\ .h5mu files. \n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "singlecpu"
|
||||
- "lowmem"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.12-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/dataflow/split_modalities/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/dataflow/split_modalities"
|
||||
executable: "target/executable/dataflow/split_modalities/split_modalities"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,12 +0,0 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,223 +0,0 @@
|
||||
name: "bcl2fastq"
|
||||
namespace: "demux"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Toni Verbeiren"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
github: "tverbeiren"
|
||||
linkedin: "verbeiren"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist and CEO"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
- "--runfolder_dir"
|
||||
description: "Input run directory"
|
||||
info: null
|
||||
example:
|
||||
- "bcl_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_sheet"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Pointer to the sample sheet"
|
||||
info: null
|
||||
example:
|
||||
- "SampleSheet.csv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output directory containig fastq files"
|
||||
info: null
|
||||
example:
|
||||
- "fastq_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--reports"
|
||||
description: "Reports directory"
|
||||
info: null
|
||||
example:
|
||||
- "reports_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--ignore_missing"
|
||||
info: null
|
||||
direction: "input"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Convert bcl files to fastq files using bcl2fastq.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "bcl"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "midmem"
|
||||
- "midcpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ghcr.io/data-intuitive/bcl2fastq:2.20"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/demux/bcl2fastq/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/demux/bcl2fastq"
|
||||
executable: "target/executable/demux/bcl2fastq/bcl2fastq"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,298 +0,0 @@
|
||||
name: "bcl_convert"
|
||||
namespace: "demux"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Toni Verbeiren"
|
||||
roles:
|
||||
- "author"
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
github: "tverbeiren"
|
||||
linkedin: "verbeiren"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist and CEO"
|
||||
- name: "Marijke Van Moerbeke"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
github: "mvanmoerbeke"
|
||||
orcid: "0000-0002-3097-5621"
|
||||
linkedin: "marijke-van-moerbeke-84303a34"
|
||||
organizations:
|
||||
- name: "OpenAnalytics"
|
||||
href: "https://www.openanalytics.eu"
|
||||
role: "Statistical Consultant"
|
||||
- name: "Weiwei Schultz"
|
||||
roles:
|
||||
- "contributor"
|
||||
info:
|
||||
role: "Contributor"
|
||||
organizations:
|
||||
- name: "Janssen R&D US"
|
||||
role: "Associate Director Data Sciences"
|
||||
- name: "Dorien Roosen"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dorien@data-intuitive.com"
|
||||
github: "dorien-er"
|
||||
linkedin: "dorien-roosen"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Scientist"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input run directory"
|
||||
info: null
|
||||
example:
|
||||
- "bcl_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_sheet"
|
||||
alternatives:
|
||||
- "-s"
|
||||
description: "Pointer to the sample sheet"
|
||||
info: null
|
||||
example:
|
||||
- "bcl_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output directory containig fastq files"
|
||||
info: null
|
||||
example:
|
||||
- "fastq_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--reports"
|
||||
description: "Reports directory"
|
||||
info: null
|
||||
example:
|
||||
- "reports_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--test_mode"
|
||||
description: "Should bcl-convert be run in test mode (using --first-tile-only)?"
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--strict_mode"
|
||||
description: "Abort if any files are missing."
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--tiles"
|
||||
description: "Process only a subset of tiles by a regular expression."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--exclude_tiles"
|
||||
description: "Exclude set of tiles by a regular expression"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--no_lane_splitting"
|
||||
description: "Wheter to avoid splitting FASTQ file by lane."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Convert bcl files to fastq files using bcl-convert.\nInformation about\
|
||||
\ upgrading from bcl2fastq via\nhttps://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html\n\
|
||||
and https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "bcl2"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "midmem"
|
||||
- "midcpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ghcr.io/data-intuitive/bclconvert:4.2"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/demux/bcl_convert/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/demux/bcl_convert"
|
||||
executable: "target/executable/demux/bcl_convert/bcl_convert"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
@@ -1,42 +0,0 @@
|
||||
process {
|
||||
// Default resources for components that hardly do any processing
|
||||
memory = { 2.GB * task.attempt }
|
||||
cpus = 1
|
||||
|
||||
// Retry for exit codes that have something to do with memory issues
|
||||
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
|
||||
maxRetries = 3
|
||||
maxMemory = null
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
|
||||
}
|
||||
|
||||
def get_memory(to_compare) {
|
||||
if (!process.containsKey("maxMemory") || !process.maxMemory) {
|
||||
return to_compare
|
||||
}
|
||||
|
||||
try {
|
||||
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
|
||||
return process.maxMemory
|
||||
}
|
||||
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
|
||||
return max_memory as nextflow.util.MemoryUnit
|
||||
}
|
||||
else {
|
||||
return to_compare
|
||||
}
|
||||
} catch (all) {
|
||||
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
|
||||
System.exit(1)
|
||||
}
|
||||
}
|
||||
@@ -1,267 +0,0 @@
|
||||
name: "cellranger_atac_mkfastq"
|
||||
namespace: "demux"
|
||||
version: "dev"
|
||||
authors:
|
||||
- name: "Vladimir Shitov"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Contributor"
|
||||
links:
|
||||
email: "vladimir.shitov@helmholtz-muenchen.de"
|
||||
github: "vladimirshitov"
|
||||
orcid: "0000-0002-1960-8812"
|
||||
linkedin: "vladimir-shitov-9a659513b"
|
||||
organizations:
|
||||
- name: "Helmholtz Munich"
|
||||
href: "https://www.helmholtz-munich.de"
|
||||
role: "PhD Candidate"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "Path of Illumina BCL run folder."
|
||||
info: null
|
||||
example:
|
||||
- "/path/to/bcl"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--csv"
|
||||
description: "The path to the simple layout sample sheet."
|
||||
info: null
|
||||
example:
|
||||
- "SampleSheet.csv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--lanes"
|
||||
description: "bcl2fastq option. Semicolon-delimited series of lanes to demultiplex.\
|
||||
\ Use this if you have a sample sheet for an entire flow cell but only want\
|
||||
\ to generate a few lanes for further 10x Genomics analysis."
|
||||
info: null
|
||||
example:
|
||||
- "1,3"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "string"
|
||||
name: "--use_bases_mask"
|
||||
description: "bcl2fastq option. Use to clip extra bases off a read if you ran\
|
||||
\ extra cycles for QC."
|
||||
info: null
|
||||
example:
|
||||
- "y50n,I6n,Y50n"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "boolean_true"
|
||||
name: "--delete_undetermined"
|
||||
description: "bcl2fastq option. Delete the Undetermined FASTQs generated by bcl2fastq.\
|
||||
\ Useful if you are demultiplexing a small number of samples from a large flow\
|
||||
\ cell."
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--barcode_mismatches"
|
||||
description: "bcl2fastq option. Use this option to change the number of allowed\
|
||||
\ mismatches per index adapter (0, 1, 2)."
|
||||
info: null
|
||||
default:
|
||||
- 1
|
||||
required: false
|
||||
min: 0
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
description: "The folder to store the demux results"
|
||||
info: null
|
||||
example:
|
||||
- "/path/to/output"
|
||||
default:
|
||||
- "fastqs"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--reports"
|
||||
description: "Reports directory"
|
||||
info: null
|
||||
example:
|
||||
- "reports_dir"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Demultiplex raw sequencing data for ATAC experiments"
|
||||
usage: "cellranger_atac_mkfastq \\\n --input /path/to/bcl \\\n --csv simple_layout_sample_sheet.csv\
|
||||
\ \\\n --output /path/to/output\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "cellranger_atac_tiny_bcl"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "highmem"
|
||||
- "highcpu"
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ghcr.io/data-intuitive/cellranger_atac:2.1"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "dev"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "DEBIAN_FRONTEND=noninteractive apt update \\\n&& apt upgrade -y && apt install\
|
||||
\ -y procps && rm -rf /var/lib/apt/lists/*\n"
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/demux/cellranger_atac_mkfastq/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/demux/cellranger_atac_mkfastq"
|
||||
executable: "target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
||||
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1926-g2dbe3b72"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "dev"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'dev'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
File diff suppressed because it is too large
Load Diff
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user