task_ist_preprocessing/scripts/run_benchmark/run_full_local.sh at 6f76c6c0588a65fa085bd039170edbd7c66559c1 · openproblems-bio/task_ist_preprocessing · GitHub

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#!/bin/bash

# get the root of the directory
REPO_ROOT=$(git rev-parse --show-toplevel)

# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

# NOTE: depending on the the datasets and components, you may need to launch this workflow
# on a different compute platform (e.g. a HPC, AWS Cloud, Azure Cloud, Google Cloud).
# please refer to the nextflow information for more details:
# https://www.nextflow.io/docs/latest/

set -e

echo "Running benchmark on test data"
echo "  Make sure to run 'scripts/project/build_all_docker_containers.sh'!"

# generate a unique id
RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
publish_dir="resources/results/${RUN_ID}"

cat > /tmp/params_settings.yaml << HERE
default_methods:
  - custom_segmentation
  - basic_transcript_assignment
  - basic_count_aggregation
  - basic_qc_filter
  - alpha_shapes
  - normalize_by_volume
  - ssam
  - no_correction
segmentation_methods:
  - custom_segmentation
  # - cellpose
  - binning
  # - stardist
  # - watershed
transcript_assignment_methods:
  - basic_transcript_assignment
  #- baysor
  # - clustermap
  # - pciseq
  # - comseg
  # - proseg
count_aggregation_methods:
  - basic_count_aggregation
qc_filtering_methods:
  - basic_qc_filter
volume_calculation_methods:
  - alpha_shapes
normalization_methods:
  - normalize_by_volume
  # - normalize_by_counts
  # - spanorm
celltype_annotation_methods:
  - ssam
  # - tacco
  # - moscot
  # - mapmycells
  # - tangram
  # - singler
  # - rctd
expression_correction_methods:
  - no_correction
  # - gene_efficiency_correction
  # - resolvi_correction
  # - split
method_parameters_yaml: /tmp/method_params.yaml
HERE

# write the parameters to file
cat > /tmp/params.yaml << HERE
input_states: resources/datasets/**/state.yaml
rename_keys: 'input_sc:output_sc;input_sp:output_sp'
save_spatial_data: false
settings: '$(yq -o json /tmp/params_settings.yaml | jq -c .)'
output_state: "state.yaml"
publish_dir: "$publish_dir"
HERE

cat > /tmp/method_params.yaml << HERE
parameters:
  binning:
    default:
      bin_size: 30
    sweep:
      bin_size: [20, 30, 40]
HERE

# run the benchmark
nextflow run . \
  -main-script target/nextflow/workflows/run_benchmark/main.nf \
  -profile docker \
  -resume \
  -entry auto \
  -c common/nextflow_helpers/labels_ci.config \
  -params-file /tmp/params.yaml