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update test snapshots
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@suzannejin
suzannejin committed Jan 16, 2025
1 parent 65ea9e5 commit 5454a7d
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Showing 2 changed files with 85 additions and 56 deletions.
8 changes: 4 additions & 4 deletions subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -296,7 +296,7 @@ nextflow_workflow {
.map { meta, results ->
def meta_new = meta - ['method': meta.method]
meta_new.method_de = meta.method
[meta, results, 'grea']
[meta_new, results, 'grea']
}
ch_gene_sets = Channel.of([
[ id:'test' ],
Expand Down Expand Up @@ -404,19 +404,19 @@ nextflow_workflow {
.map { meta, results ->
def meta_new = meta - ['method': meta.method]
meta_new.method_de = meta.method
[meta, results, 'gprofiler2']
[meta_new, results, 'gprofiler2']
}
ch_input_for_gsea = ABUNDANCE_DIFFERENTIAL_FILTER.out.normalised_matrix
.map { meta, results ->
def meta_new = meta - ['method': meta.method]
meta_new.method_de = meta.method
[meta, results, 'gsea']
[meta_new, results, 'gsea']
}
ch_input_for_grea = ABUNDANCE_DIFFERENTIAL_FILTER.out.adjacency
.map { meta, results ->
def meta_new = meta - ['method': meta.method]
meta_new.method_de = meta.method
[meta, results, 'grea']
[meta_new, results, 'grea']
}
ch_input = ch_input_for_gprofiler2
.mix(ch_input_for_gsea)
Expand Down
133 changes: 81 additions & 52 deletions subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
"treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92"
],
Expand All @@ -23,10 +23,24 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "limma"
"method_de": "limma",
"method": "gprofiler2"
},
"treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
{
"id": "treatment_mCherry_hND6__test",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"fc_threshold": 1.5,
"stat_threshold": 100,
"method_de": "propd",
"method": "gprofiler2"
},
"treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
Expand All @@ -37,10 +51,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
"treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c"
],
Expand All @@ -51,10 +65,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "limma"
"method_de": "limma",
"method": "gprofiler2"
},
"treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
],
Expand All @@ -65,10 +79,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gprofiler2",
"method_de": "propd",
"fc_threshold": 1.5,
"stat_threshold": 100
"stat_threshold": 100,
"method_de": "propd",
"method": "gprofiler2"
},
"treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
Expand All @@ -81,10 +95,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
[
"treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca",
Expand All @@ -100,10 +114,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
[
"treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725",
Expand All @@ -121,55 +135,55 @@
[
[
{
"id": "treatment_mCherry_hND6_",
"id": "treatment_mCherry_hND6__test",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method_de": "deseq2",
"method": "gsea"
},
"treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0"
"treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0"
],
[
{
"id": "treatment_mCherry_hND6_",
"id": "treatment_mCherry_hND6__test",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method_de": "limma",
"method": "gsea"
},
"treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074"
"treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074"
],
[
{
"id": "treatment_mCherry_hND6_sample_number",
"id": "treatment_mCherry_hND6_sample_number_test",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method_de": "deseq2",
"method": "gsea"
},
"treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0"
"treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0"
],
[
{
"id": "treatment_mCherry_hND6_sample_number",
"id": "treatment_mCherry_hND6_sample_number_test",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method_de": "limma",
"method": "gsea"
},
"treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074"
"treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,a4dcc9581c9c63d35ef32ee0df882074"
]
],
[
Expand All @@ -180,8 +194,8 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "grea",
"method_de": "propd"
"method_de": "propd",
"method": "grea"
},
"treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697"
],
Expand All @@ -192,26 +206,41 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "grea",
"method_de": "propd"
"method_de": "propd",
"method": "grea"
},
"treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697"
]
],
[
"versions.yml:md5,25ab98049a601f4940f3e5a24aa73f55",
"versions.yml:md5,25ab98049a601f4940f3e5a24aa73f55",
"versions.yml:md5,25ab98049a601f4940f3e5a24aa73f55",
"versions.yml:md5,25ab98049a601f4940f3e5a24aa73f55",
"versions.yml:md5,266a82ff5781032b94f374685afd8568",
"versions.yml:md5,266a82ff5781032b94f374685afd8568",
"versions.yml:md5,266a82ff5781032b94f374685afd8568",
"versions.yml:md5,266a82ff5781032b94f374685afd8568",
"versions.yml:md5,7861e3047b941b86ef50124168a13b51",
"versions.yml:md5,7861e3047b941b86ef50124168a13b51",
"versions.yml:md5,7861e3047b941b86ef50124168a13b51",
"versions.yml:md5,7861e3047b941b86ef50124168a13b51",
"versions.yml:md5,7861e3047b941b86ef50124168a13b51",
"versions.yml:md5,7861e3047b941b86ef50124168a13b51",
"versions.yml:md5,cd9cd1563a983e586b15fd2276da8bfb",
"versions.yml:md5,cd9cd1563a983e586b15fd2276da8bfb",
"versions.yml:md5,e3febf7ecd8d1f111e2d38f9e3c37b2a",
"versions.yml:md5,e3febf7ecd8d1f111e2d38f9e3c37b2a",
"versions.yml:md5,e3febf7ecd8d1f111e2d38f9e3c37b2a",
"versions.yml:md5,e3febf7ecd8d1f111e2d38f9e3c37b2a",
"versions.yml:md5,f2db818ec8143f64399247548098b643"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-16T14:16:36.808895029"
"timestamp": "2025-01-16T15:53:32.61356774"
},
"deseq2 + gprofiler2 - mouse": {
"content": [
Expand All @@ -223,10 +252,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
"treatment_mCherry_hND6__test.gprofiler2.all_enriched_pathways.tsv:md5,d586d92fb6cc3e41d493d14c4d9a7d92"
],
Expand All @@ -237,10 +266,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
"treatment_mCherry_hND6_sample_number_test.gprofiler2.all_enriched_pathways.tsv:md5,fa880c70d06f56d8dad0ac8078e6233c"
]
Expand All @@ -253,10 +282,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
[
"treatment_mCherry_hND6__test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,4c95059438af872253aa95a5ff127fca",
Expand All @@ -272,10 +301,10 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gprofiler2",
"fc_threshold": 1.5,
"stat_threshold": 0.05,
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gprofiler2"
},
[
"treatment_mCherry_hND6_sample_number_test.gprofiler2.GO:BP.sub_enriched_pathways.tsv:md5,dc27af1c941636f8b03e8c8724773725",
Expand All @@ -302,7 +331,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-13T13:11:00.283653303"
"timestamp": "2025-01-16T15:45:53.413217372"
},
"propd + grea - mouse": {
"content": [
Expand All @@ -314,8 +343,8 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "grea",
"method_de": "propd"
"method_de": "propd",
"method": "grea"
},
"treatment_mCherry_hND6__test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697"
],
Expand All @@ -326,8 +355,8 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "grea",
"method_de": "propd"
"method_de": "propd",
"method": "grea"
},
"treatment_mCherry_hND6_sample_number_test.grea.tsv:md5,786faeccf39926d2f7c980ef549a2697"
]
Expand All @@ -342,7 +371,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-13T15:52:21.255071921"
"timestamp": "2025-01-16T15:49:48.620415775"
},
"test gprofiler2 - mouse": {
"content": [
Expand Down Expand Up @@ -397,7 +426,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-13T11:50:25.895189209"
"timestamp": "2025-01-16T15:44:46.811837071"
},
"deseq2 + gsea - mouse": {
"content": [
Expand All @@ -409,8 +438,8 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "",
"method": "gsea",
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gsea"
},
"treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6__test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0"
Expand All @@ -422,8 +451,8 @@
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number",
"method": "gsea",
"method_de": "deseq2"
"method_de": "deseq2",
"method": "gsea"
},
"treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_mCherry.tsv:md5,ce8792382ae299749445767ff16aaecc",
"treatment_mCherry_hND6_sample_number_test.mh.all.v2022.1.Mm.symbols.gsea_report_for_hND6.tsv:md5,354a961c7e1417db2bf1f7e8d00c54f0"
Expand All @@ -439,6 +468,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-14T15:21:26.781608773"
"timestamp": "2025-01-16T15:46:48.409198412"
}
}

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