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tests: switch reml setup to makegrmpart
1 parent b9a9306 commit 63b9057

2 files changed

Lines changed: 52 additions & 49 deletions

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‎modules/nf-core/gcta/reml/tests/helpers/makegrm/main.nf‎

Lines changed: 0 additions & 36 deletions
This file was deleted.

‎modules/nf-core/gcta/reml/tests/main.nf.test‎

Lines changed: 52 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ nextflow_process {
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tag "modules_nfcore"
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tag "gcta"
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tag "gcta/reml"
11-
tag "tests/helpers/makegrm"
11+
tag "gcta/makegrmpart"
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tag "gawk"
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setup {
@@ -68,15 +68,24 @@ nextflow_process {
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}
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}
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71-
run("GCTA_MAKEGRM_HELPER", alias: "GCTA_MAKEGRM_DENSE") {
72-
script "../tests/helpers/makegrm/main.nf"
71+
run("GCTA_MAKEGRMPART", alias: "GCTA_MAKEGRMPART_DENSE") {
72+
script "../../makegrmpart/main.nf"
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process {
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"""
75+
file('plink_simulated.mbfile').text = 'plink_simulated\\n'
76+
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input[0] = [
76-
[ id:'plink_simulated_dense.part_1_1' ],
77-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
78-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
79-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
78+
[ id:'plink_simulated_dense', part_gcta_job:1, nparts_gcta:1 ],
79+
file('plink_simulated.mbfile'),
80+
[
81+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
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],
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[
84+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
85+
],
86+
[
87+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
88+
]
8089
]
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input[1] = [[ id:'all_variants' ], []]
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"""
@@ -89,8 +98,13 @@ nextflow_process {
8998
when {
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process {
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"""
101+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
102+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
103+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
104+
}
105+
92106
input[0] = GAWK_MULTI_PHENOTYPES.out.output.map { meta, pheno -> [[ id:'QuantitativeTraitMpheno2' ], pheno] }
93-
input[1] = GCTA_MAKEGRM_DENSE.out.grm_files
107+
input[1] = dense_grm
94108
input[2] = GAWK_QUANTITATIVE_COVARIATES.out.output
95109
input[3] = GAWK_CATEGORICAL_COVARIATES.out.output
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input[4] = 2
@@ -118,8 +132,13 @@ nextflow_process {
118132
when {
119133
process {
120134
"""
135+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
136+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
137+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
138+
}
139+
121140
input[0] = GAWK_QUANTITATIVE_PHENOTYPE.out.output
122-
input[1] = GCTA_MAKEGRM_DENSE.out.grm_files
141+
input[1] = dense_grm
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input[2] = GAWK_QUANTITATIVE_COVARIATES.out.output
124143
input[3] = GAWK_CATEGORICAL_COVARIATES.out.output
125144
input[4] = 1
@@ -147,8 +166,13 @@ nextflow_process {
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when {
148167
process {
149168
"""
169+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
170+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
171+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
172+
}
173+
150174
input[0] = GAWK_QUANTITATIVE_PHENOTYPE.out.output
151-
input[1] = GCTA_MAKEGRM_DENSE.out.grm_files
175+
input[1] = dense_grm
152176
input[2] = [[ id:'covariates_quant' ], []]
153177
input[3] = [[ id:'covariates_cat' ], []]
154178
input[4] = 1
@@ -176,8 +200,13 @@ nextflow_process {
176200
when {
177201
process {
178202
"""
203+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
204+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
205+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
206+
}
207+
179208
input[0] = GAWK_MULTI_PHENOTYPES.out.output.map { meta, pheno -> [[ id:'QuantitativeTraitMphenoDefault' ], pheno] }
180-
input[1] = GCTA_MAKEGRM_DENSE.out.grm_files
209+
input[1] = dense_grm
181210
input[2] = GAWK_QUANTITATIVE_COVARIATES.out.output
182211
input[3] = GAWK_CATEGORICAL_COVARIATES.out.output
183212
input[4] = []
@@ -205,8 +234,13 @@ nextflow_process {
205234
when {
206235
process {
207236
"""
237+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
238+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
239+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
240+
}
241+
208242
input[0] = GAWK_MULTI_PHENOTYPES.out.output.map { meta, pheno -> [[ id:'QuantitativeTraitInvalidMpheno' ], pheno] }
209-
input[1] = GCTA_MAKEGRM_DENSE.out.grm_files
243+
input[1] = dense_grm
210244
input[2] = GAWK_QUANTITATIVE_COVARIATES.out.output
211245
input[3] = GAWK_CATEGORICAL_COVARIATES.out.output
212246
input[4] = 3
@@ -229,8 +263,13 @@ nextflow_process {
229263
when {
230264
process {
231265
"""
266+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
267+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
268+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
269+
}
270+
232271
input[0] = GAWK_QUANTITATIVE_PHENOTYPE.out.output
233-
input[1] = GCTA_MAKEGRM_DENSE.out.grm_files
272+
input[1] = dense_grm
234273
input[2] = [[ id:'covariates_quant' ], []]
235274
input[3] = [[ id:'covariates_cat' ], []]
236275
input[4] = 1

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