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Try and Fix Integration Tests #126

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merged 1 commit into from
Oct 11, 2023
Merged

Try and Fix Integration Tests #126

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2 changes: 1 addition & 1 deletion nextflow/modules/bayestme/bayestme_spatial_expression/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ process BAYESTME_SPATIAL_EXPRESSION {

plot_spatial_expression \
--deconvolution-result ${deconvolution_samples} \
--sde-samples ${prefix}/sde_samples.h5 \
--sde-result ${prefix}/sde_samples.h5 \
--output-dir ${prefix}/plots \
${args2}

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2 changes: 1 addition & 1 deletion nextflow/tests/data/test_spaceranger_data/spatial/tissue_positions_list.csv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
AAACAACGAATAGTTC-1,1,0,0,4650,12203
AAACAAGTATCTCCCA-1,1,1,1,4887,12338
AAACAATCTACTAGCA-1,1,0,2,4651,12475
AAACAATCTACTAGCA-1,0,0,2,4651,12475
6 changes: 3 additions & 3 deletions nextflow/tests/modules/bayestme/bayestme_bleeding_correction/test.yml
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Expand Up @@ -3,6 +3,6 @@
tags:
- bayestme_bleeding_correction
files:
- path: output/bleed_correction_results.h5
- path: output/dataset_corrected.h5ad
- path: output/plots/basis-functions.pdf
- path: output/test/bleed_correction_results.h5
- path: output/test/dataset_corrected.h5ad
- path: output/test/plots/basis-functions.pdf
2 changes: 1 addition & 1 deletion nextflow/tests/modules/bayestme/bayestme_deconvolution/main.nf
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Expand Up @@ -7,7 +7,7 @@ workflow bayestme_deconvolution {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['bayestme']['filtered_dataset'], checkIfExists: true),
5,
1.0,
100.0,
[]
]
BAYESTME_DECONVOLUTION ( input )
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2 changes: 1 addition & 1 deletion nextflow/tests/modules/bayestme/bayestme_filter_genes/test.yml
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Expand Up @@ -3,4 +3,4 @@
tags:
- bayestme_filter_genes
files:
- path: output/dataset_filtered.h5ad
- path: output/test/dataset_filtered.h5ad
2 changes: 1 addition & 1 deletion nextflow/tests/modules/bayestme/bayestme_load_spaceranger/test.yml
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Expand Up @@ -3,4 +3,4 @@
tags:
- bayestme_load_spaceranger
files:
- path: output/dataset.h5ad
- path: output/test/dataset.h5ad
2 changes: 1 addition & 1 deletion nextflow/tests/modules/bayestme/bayestme_phenotype_selection/test.yml
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Expand Up @@ -3,4 +3,4 @@
tags:
- bayestme_phenotype_selection
files:
- path: output/fold_0.h5ad
- path: output/test/fold_0.h5ad
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