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Unittest for Amplicon Coverage – Snakemake Unitetest CI #34

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Oct 25, 2024
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Merged

Unittest for Amplicon Coverage – Snakemake Unitetest CI #34

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e6ff3d5
fix wrongly typed file
gordonkoehn Oct 17, 2024
97e0ebd
update the references accordingly
gordonkoehn Oct 17, 2024
d7281e6
adding integration unittest data - subset of test_output_sars-cov-2 a…
gordonkoehn Oct 17, 2024
51fb393
addding primer scheme for unittest
gordonkoehn Oct 17, 2024
d9aedb9
WIP
gordonkoehn Oct 24, 2024
8fe59ef
adding unit tests
gordonkoehn Oct 24, 2024
9185d5b
formating
gordonkoehn Oct 24, 2024
3760a09
cleanup
gordonkoehn Oct 25, 2024
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14 changes: 0 additions & 14 deletions config/amplicon_cov.smk
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This file was deleted.

15 changes: 15 additions & 0 deletions config/amplicon_cov.yaml
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#### Parameters
# The name of the batch to process
batch: "20200729"

###### Inputs
# where to find the list of samples i.e. samples.tsv
sample_list_dir: "workflow/.tests/unit/amplicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/"

# where to find the samples from the list
sample_dir: "workflow/.tests/unit/amplicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/results"
# bed file with the primers
primers_fp: "workflow/.tests/unit/amplicon_cov/data/primer_schemes/articV3primers.bed"

##### Outputs
output_dir: "results/"
3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -13,7 +13,8 @@ matplotlib = "^3.9.2"
seaborn = "^0.13.2"
pandas-stubs = "^2.2.2.240807"
click = "^8.1.7"
snakemake = "^8.20.4"
# Pinned as later snakemake version fail to unit test generation
snakemake = "8.18.1"

[tool.poetry.group.dev.dependencies]
pytest = "^7.2.1"
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15 changes: 15 additions & 0 deletions workflow/.tests/unit/amplicon_cov/amplicon_cov.yaml
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#### Parameters
# The name of the batch to process
batch: "20200729"

###### Inputs
# where to find the list of samples i.e. samples.tsv
sample_list_dir: "data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/"

# where to find the samples from the list
sample_dir: "data/subset_vpipe_smkdeploy/test_output_sars-cov-2/results"
# bed file with the primers
primers_fp: "data/primer_schemes/articV3primers.bed"

##### Outputs
output_dir: ""
219 changes: 219 additions & 0 deletions workflow/.tests/unit/amplicon_cov/data/primer_schemes/articV3primers.bed
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13 changes: 13 additions & 0 deletions workflow/.tests/unit/amplicon_cov/data/subset_vpipe_smkdeploy/README.md
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This firectory contains test data from the V-Pipe snakedeploy builds run on the rubicon branch:

https://github.com/cbg-ethz/V-pipe/actions/runs/11176196539

The data are the artefacts of these github actions repesenting intemediate results of V-Pipe processing.

This folder currently contains:
- test_output_sars-cov-2
- results/*/*/aligments/coverage.tsv.gz
- samples/samples.tsv



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2 changes: 2 additions & 0 deletions .../unit/amplicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/samples.tsv
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pos_MN908947_3_1 20200729 250 v3
pos_MT007544_1_1 20200729 250 v3
2 changes: 2 additions & 0 deletions ...plicon_cov/data/subset_vpipe_smkdeploy/test_output_sars-cov-2/samples/samples20200729.tsv
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pos_MN908947_3_1 20200729 250 v3
pos_MT007544_1_1 20200729 250 v3
3 changes: 3 additions & 0 deletions workflow/.tests/unit/amplicon_cov/expected/20200729/amplicons_coverages.csv
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@@ -0,0 +1,3 @@
sample,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97
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