task_ist_preprocessing/scripts/run_benchmark/run_test_seqeracloud.sh at 6dc3aa8c0d659dcc536a48d92d94e8477eafd621 · openproblems-bio/task_ist_preprocessing · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
#!/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"

set -e

resources_test_s3=s3://openproblems-data/resources_test/task_ist_preprocessing
publish_dir_s3="s3://openproblems-nextflow/temp/results/$(date +%Y-%m-%d_%H-%M-%S)"

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
#method_parameters_yaml: /tmp/method_params.yaml
HERE

# Write the parameters to file (input_states version, NOTE: enable `-entry_name auto` for this)
cat > /tmp/params.yaml << HERE
input_states: $resources_test_s3/**/state.yaml
rename_keys: 'input_sc:output_sc;input_sp:output_sp'
save_spatial_data: false
settings: '$(yq -o json /tmp/params_settings.yaml | jq -c .)'
output_state: "state.yaml"
publish_dir: "$publish_dir_s3"
HERE

# # write the parameters to file (specific id version, NOTE: disable `-entry_name auto` for this)
# cat > /tmp/params.yaml << HERE
# id: mouse_brain_combined
# input_sc: $resources_test_s3/mouse_brain_combined/scrnaseq_reference.h5ad
# input_sp: $resources_test_s3/mouse_brain_combined/raw_ist.zarr
# save_spatial_data: false
# settings: '$(yq -o json /tmp/params_settings.yaml | jq -c .)'
# output_state: "state.yaml"
# publish_dir: $publish_dir_s3
# HERE

# NOTE: this file needs to be made available on the seqera cloud workspace and the
#       path needs to be added above (method_parameters_yaml)
cat > /tmp/method_params.yaml << HERE
parameters:
  binning:
    default:
      bin_size: 30
    sweep:
      bin_size: [20, 30, 40]
HERE


tw launch https://github.com/openproblems-bio/task_ist_preprocessing.git \
  --revision build/main \
  --pull-latest \
  --main-script target/nextflow/workflows/run_benchmark/main.nf \
  --workspace 53907369739130 \
  --params-file /tmp/params.yaml \
  --entry-name auto \
  --config common/nextflow_helpers/labels_tw.config \
  --labels task_ist_preprocessing,test

# aws s3 sync \
#   s3://openproblems-nextflow/temp/results \
#   temp_results \
#   --profile op \
#   --dryrun