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Merge pull request #454 from atrigila/fix_test_edger
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Fix test edgeR
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@atrigila
atrigila authored Oct 1, 2024
2 parents 2016dac + 4c3e85c commit 19a1c8b
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Showing 2 changed files with 59 additions and 107 deletions.
25 changes: 20 additions & 5 deletions modules/local/edger_qc/tests/edger_qc.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,15 @@ nextflow_process {
}

then {
assert process.success
assert snapshot(process.out).match()
assertAll(
{ assert process.success },
{ assert snapshot(
// Snapshot only the stable files (.txt, .csv) and exclude PDFs
process.out.edger_files.get(0).findAll { !it.endsWith('pdf')},
process.out.versions
)
.match() }
)
}

}
Expand Down Expand Up @@ -49,10 +56,18 @@ nextflow_process {
}

then {
assert process.success
assert snapshot(process.out).match()
assertAll(
{ assert process.success },
{ assert snapshot(
// Snapshot only the stable files (.txt, .csv) and exclude PDFs
process.out.edger_files.get(0).findAll { !it.endsWith('pdf')},
process.out.versions,
// Check MDS plot exists
file(process.out.edger_files[0].find { file(it).name == "hairpin_edgeR_MDS_plot.pdf" }).exists()
)
.match() }
)
}

}

}
141 changes: 39 additions & 102 deletions modules/local/edger_qc/tests/edger_qc.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,120 +1,57 @@
{
"Should not produce MDS plot": {
"content": [
{
"0": [
[
"hairpin_counts.csv:md5,9a2c4c71862349eee5071cf08a81df52",
"hairpin_logtpm.csv:md5,590516d1c7447023933f055446d34552",
"hairpin_logtpm.txt:md5,5cbb1258c290d958910db677490596c0",
"hairpin_normalized_CPM.txt:md5,2f6685750d4c0aa1dc8150276f8a5a2d",
"hairpin_unmapped_read_counts.txt:md5,b3ca3b9f01dbdab1bdbd989769121794",
"mature_counts.csv:md5,17b953ef2fb4e58d83acc263f68755fd",
"mature_logtpm.csv:md5,b4654e4ec264243156b1ceab73503017",
"mature_logtpm.txt:md5,9cba6dd8336de7fe79be641285e92a73",
"mature_normalized_CPM.txt:md5,43db2854ec00e6afca25883b64ad67bd",
"mature_unmapped_read_counts.txt:md5,0e129ffe42aa32f96250a5071d3a7649"
]
],
"1": [
"versions.yml:md5,2e5b1dd3ed5befd1d4c9812a3fcb768a"
],
"edger_files": [
[
"hairpin_counts.csv:md5,9a2c4c71862349eee5071cf08a81df52",
"hairpin_logtpm.csv:md5,590516d1c7447023933f055446d34552",
"hairpin_logtpm.txt:md5,5cbb1258c290d958910db677490596c0",
"hairpin_normalized_CPM.txt:md5,2f6685750d4c0aa1dc8150276f8a5a2d",
"hairpin_unmapped_read_counts.txt:md5,b3ca3b9f01dbdab1bdbd989769121794",
"mature_counts.csv:md5,17b953ef2fb4e58d83acc263f68755fd",
"mature_logtpm.csv:md5,b4654e4ec264243156b1ceab73503017",
"mature_logtpm.txt:md5,9cba6dd8336de7fe79be641285e92a73",
"mature_normalized_CPM.txt:md5,43db2854ec00e6afca25883b64ad67bd",
"mature_unmapped_read_counts.txt:md5,0e129ffe42aa32f96250a5071d3a7649"
]
],
"versions": [
"versions.yml:md5,2e5b1dd3ed5befd1d4c9812a3fcb768a"
]
}
[
"hairpin_counts.csv:md5,9a2c4c71862349eee5071cf08a81df52",
"hairpin_logtpm.csv:md5,590516d1c7447023933f055446d34552",
"hairpin_logtpm.txt:md5,5cbb1258c290d958910db677490596c0",
"hairpin_normalized_CPM.txt:md5,2f6685750d4c0aa1dc8150276f8a5a2d",
"hairpin_unmapped_read_counts.txt:md5,b3ca3b9f01dbdab1bdbd989769121794",
"mature_counts.csv:md5,17b953ef2fb4e58d83acc263f68755fd",
"mature_logtpm.csv:md5,b4654e4ec264243156b1ceab73503017",
"mature_logtpm.txt:md5,9cba6dd8336de7fe79be641285e92a73",
"mature_normalized_CPM.txt:md5,43db2854ec00e6afca25883b64ad67bd",
"mature_unmapped_read_counts.txt:md5,0e129ffe42aa32f96250a5071d3a7649"
],
[
"versions.yml:md5,2e5b1dd3ed5befd1d4c9812a3fcb768a"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-20T15:35:12.666335127"
"timestamp": "2024-09-30T19:57:28.863043452"
},
"Should produce MDS plot": {
"content": [
{
"0": [
[
"hairpin_CPM_heatmap.pdf:md5,5d7ade334680f6fa7f822c9c5059ee97",
"hairpin_counts.csv:md5,4b0fa0e52a7b8b40bdc5930378430136",
"hairpin_edgeR_MDS_distance_matrix.txt:md5,f0eb20be2b7bae7775ef65e03139f5a9",
"hairpin_edgeR_MDS_plot.pdf:md5,27c8a310bdfd200f37068c9fddb80d17",
"hairpin_edgeR_MDS_plot_coordinates.txt:md5,2f1f865b11c4ee5253f80ebe9a1914ee",
"hairpin_log2CPM_sample_distances.txt:md5,20592bfa42e23827dfac02eab1e033ff",
"hairpin_log2CPM_sample_distances_dendrogram.pdf:md5,1bfcdd534efcb49b167ef29981f325ce",
"hairpin_log2CPM_sample_distances_heatmap.pdf:md5,2e8e51bd4778a644bce4c0253f683c0b",
"hairpin_logtpm.csv:md5,35a5449d3468995e8010907105922898",
"hairpin_logtpm.txt:md5,1de707003b6ed2c38372670d69eaf5fb",
"hairpin_normalized_CPM.txt:md5,d42e8eb89175107c5dfbfb2c7da98d37",
"hairpin_unmapped_read_counts.txt:md5,c587147fb1a5b6681c17eff2d4859022",
"mature_CPM_heatmap.pdf:md5,486f30379c552346025d9f25eb9a2e52",
"mature_counts.csv:md5,f961a9d6749dbf0c84dfb8976e0b6516",
"mature_edgeR_MDS_distance_matrix.txt:md5,bfbf327feedbc2e7bbbd57020ae0594c",
"mature_edgeR_MDS_plot.pdf:md5,9f9e312f882ff7e7de70701af4dd0f6b",
"mature_edgeR_MDS_plot_coordinates.txt:md5,b89854153c61a348929ea3901a61bd56",
"mature_log2CPM_sample_distances.txt:md5,b4ed17084de4711e7fd4a12d221d65ec",
"mature_log2CPM_sample_distances_dendrogram.pdf:md5,03c1ff39c90fbc64a1112d93756592fa",
"mature_log2CPM_sample_distances_heatmap.pdf:md5,e4dc113bae6464ad0b914f173f8042b1",
"mature_logtpm.csv:md5,850a8ed0e4559d338578f81dc849acf5",
"mature_logtpm.txt:md5,9087155e2f4bc7f85ced8ab8c02c77e6",
"mature_normalized_CPM.txt:md5,3bc348a1248f9597dfc9e8e465c3c8a8",
"mature_unmapped_read_counts.txt:md5,138cf290420edbf9721b9db861204c9c"
]
],
"1": [
"versions.yml:md5,2e5b1dd3ed5befd1d4c9812a3fcb768a"
],
"edger_files": [
[
"hairpin_CPM_heatmap.pdf:md5,5d7ade334680f6fa7f822c9c5059ee97",
"hairpin_counts.csv:md5,4b0fa0e52a7b8b40bdc5930378430136",
"hairpin_edgeR_MDS_distance_matrix.txt:md5,f0eb20be2b7bae7775ef65e03139f5a9",
"hairpin_edgeR_MDS_plot.pdf:md5,27c8a310bdfd200f37068c9fddb80d17",
"hairpin_edgeR_MDS_plot_coordinates.txt:md5,2f1f865b11c4ee5253f80ebe9a1914ee",
"hairpin_log2CPM_sample_distances.txt:md5,20592bfa42e23827dfac02eab1e033ff",
"hairpin_log2CPM_sample_distances_dendrogram.pdf:md5,1bfcdd534efcb49b167ef29981f325ce",
"hairpin_log2CPM_sample_distances_heatmap.pdf:md5,2e8e51bd4778a644bce4c0253f683c0b",
"hairpin_logtpm.csv:md5,35a5449d3468995e8010907105922898",
"hairpin_logtpm.txt:md5,1de707003b6ed2c38372670d69eaf5fb",
"hairpin_normalized_CPM.txt:md5,d42e8eb89175107c5dfbfb2c7da98d37",
"hairpin_unmapped_read_counts.txt:md5,c587147fb1a5b6681c17eff2d4859022",
"mature_CPM_heatmap.pdf:md5,486f30379c552346025d9f25eb9a2e52",
"mature_counts.csv:md5,f961a9d6749dbf0c84dfb8976e0b6516",
"mature_edgeR_MDS_distance_matrix.txt:md5,bfbf327feedbc2e7bbbd57020ae0594c",
"mature_edgeR_MDS_plot.pdf:md5,9f9e312f882ff7e7de70701af4dd0f6b",
"mature_edgeR_MDS_plot_coordinates.txt:md5,b89854153c61a348929ea3901a61bd56",
"mature_log2CPM_sample_distances.txt:md5,b4ed17084de4711e7fd4a12d221d65ec",
"mature_log2CPM_sample_distances_dendrogram.pdf:md5,03c1ff39c90fbc64a1112d93756592fa",
"mature_log2CPM_sample_distances_heatmap.pdf:md5,e4dc113bae6464ad0b914f173f8042b1",
"mature_logtpm.csv:md5,850a8ed0e4559d338578f81dc849acf5",
"mature_logtpm.txt:md5,9087155e2f4bc7f85ced8ab8c02c77e6",
"mature_normalized_CPM.txt:md5,3bc348a1248f9597dfc9e8e465c3c8a8",
"mature_unmapped_read_counts.txt:md5,138cf290420edbf9721b9db861204c9c"
]
],
"versions": [
"versions.yml:md5,2e5b1dd3ed5befd1d4c9812a3fcb768a"
]
}
[
"hairpin_counts.csv:md5,4b0fa0e52a7b8b40bdc5930378430136",
"hairpin_edgeR_MDS_distance_matrix.txt:md5,f0eb20be2b7bae7775ef65e03139f5a9",
"hairpin_edgeR_MDS_plot_coordinates.txt:md5,2f1f865b11c4ee5253f80ebe9a1914ee",
"hairpin_log2CPM_sample_distances.txt:md5,20592bfa42e23827dfac02eab1e033ff",
"hairpin_logtpm.csv:md5,35a5449d3468995e8010907105922898",
"hairpin_logtpm.txt:md5,1de707003b6ed2c38372670d69eaf5fb",
"hairpin_normalized_CPM.txt:md5,d42e8eb89175107c5dfbfb2c7da98d37",
"hairpin_unmapped_read_counts.txt:md5,c587147fb1a5b6681c17eff2d4859022",
"mature_counts.csv:md5,f961a9d6749dbf0c84dfb8976e0b6516",
"mature_edgeR_MDS_distance_matrix.txt:md5,bfbf327feedbc2e7bbbd57020ae0594c",
"mature_edgeR_MDS_plot_coordinates.txt:md5,b89854153c61a348929ea3901a61bd56",
"mature_log2CPM_sample_distances.txt:md5,b4ed17084de4711e7fd4a12d221d65ec",
"mature_logtpm.csv:md5,850a8ed0e4559d338578f81dc849acf5",
"mature_logtpm.txt:md5,9087155e2f4bc7f85ced8ab8c02c77e6",
"mature_normalized_CPM.txt:md5,3bc348a1248f9597dfc9e8e465c3c8a8",
"mature_unmapped_read_counts.txt:md5,138cf290420edbf9721b9db861204c9c"
],
[
"versions.yml:md5,2e5b1dd3ed5befd1d4c9812a3fcb768a"
],
true
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-20T15:39:22.840053942"
"timestamp": "2024-09-30T19:59:15.428541578"
}
}

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