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dummy fails
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matin authored and matin committed Jul 24, 2024

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Showing 4 changed files with 86 additions and 28 deletions.
2 changes: 1 addition & 1 deletion notebooks/preprocess.ipynb
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"outputs": [],
"source": [
"!aws s3 cp s3://openproblems-bio/public/neurips-2023-competition/sc_counts.h5ad ./resources_raw/ --no-sign-request\n",
"!aws s3 cp s3://openproblems-bio/public/neurips-2023-competition/multiome_counts.h5mu ./resources_raw/ --no-sign-request"
"aws s3 cp s3://openproblems-bio/public/neurips-2023-competition/2023-09-14_kaggle_upload/2023-08-31_sc_multiome_expression_atac.h5ad ./resources_raw/ --no-sign-request"
]
},
{
27 changes: 0 additions & 27 deletions src/methods/dummy/config.novsh.yaml

This file was deleted.

85 changes: 85 additions & 0 deletions src/methods/dummy/config.vsh.yaml
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# __merge__: ../../api/comp_method.yaml

functionality:
name: dummy
info:
label: dummy
summary: "FILL IN: A one sentence summary of this method."
description: |
A dummy method that contains the format of a real GRN inference method.
documentation_url: https://url.to/the/documentation
repository_url: https://github.com/organisation/repository
arguments:
- name: --multiomics_rna
__merge__: ../../api/file_multiomics_rna_h5ad.yaml
required: True
direction: input
- name: --multiomics_atac
__merge__: ../../api/file_multiomics_atac_h5ad.yaml
required: false
direction: input
- name: --prediction
__merge__: ../../api/file_prediction.yaml
required: true
direction: output

- name: --annotation_file
type: file
example: resources/grn-benchmark/supp/gencode.v45.annotation.gtf.gz
info:
label: annotation
summary: "annotation file"
file_type: gtf.gz
columns:
- name: gene_name
type: string
required: false
- name: annotation
type: string
required: false
required: false
direction: input
- name: --motif_file
type: file
example: resources/grn-benchmark/supp/JASPAR2022-hg38.bed.gz
info:
label: tfmotif
summary: "Tf motif info"
file_type: bed.gz
columns:
- name: tf_name
type: string
required: false
- name: region
type: string
required: false
required: false
direction: input
- name: --temp_dir
type: string
direction: input
default: output
- name: --num_workers
type: integer
direction: input
default: 4
test_resources:
- type: python_script
path: /src/common/component_tests/run_and_check_output.py
- path: /resources/grn-benchmark
dest: resources/grn-benchmark
resources:
- type: python_script
path: script.py

platforms:
- type: docker
image: ghcr.io/openproblems-bio/base_python:1.0.4
setup:
- type: python
packages: [ ]

- type: native
- type: nextflow
directives:
label: [midtime,midmem,midcpu]
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