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Use real dependency modules in fastgwa tests
1 parent e5e871a commit 4ad44fa

2 files changed

Lines changed: 58 additions & 49 deletions

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‎modules/nf-core/gcta/fastgwa/tests/helpers/gcta_prepare_sparse/main.nf‎

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

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

Lines changed: 58 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,9 @@ nextflow_process {
88
tag "modules_nfcore"
99
tag "gcta"
1010
tag "gcta/fastgwa"
11+
tag "gcta/makegrmpart"
12+
tag "gcta/makebksparse"
1113
tag "gawk"
12-
tag "tests/helpers/gcta_prepare_sparse"
1314
config "./nextflow.config"
1415

1516
setup {
@@ -83,17 +84,41 @@ nextflow_process {
8384
}
8485
}
8586

86-
run("GCTA_TEST_PREPARE_SPARSE", alias: "GCTA_TEST_PREPARE_SPARSE_DENSE") {
87-
script "../tests/helpers/gcta_prepare_sparse/main.nf"
87+
run("GCTA_MAKEGRMPART", alias: "GCTA_MAKEGRMPART_DENSE") {
88+
script "../../makegrmpart/main.nf"
8889
process {
8990
"""
91+
file('plink_simulated.mbfile').text = 'plink_simulated\\n'
92+
9093
input[0] = [
91-
[ id:'plink_simulated_dense' ],
92-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
93-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
94-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
94+
[ id:'plink_simulated_dense', part_gcta_job:1, nparts_gcta:1 ],
95+
file('plink_simulated.mbfile'),
96+
[
97+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
98+
],
99+
[
100+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
101+
],
102+
[
103+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
104+
]
95105
]
96-
input[1] = 0.05
106+
input[1] = [[ id:'all_variants' ], []]
107+
"""
108+
}
109+
}
110+
111+
run("GCTA_MAKEBKSPARSE", alias: "GCTA_MAKEBKSPARSE_DENSE") {
112+
script "../../makebksparse/main.nf"
113+
process {
114+
"""
115+
dense_grm = GCTA_MAKEGRMPART_DENSE.out.grm_files.map { meta, grm_id, grm_bin, grm_n_bin ->
116+
def prefix = meta.id + '.part_' + meta.nparts_gcta + '_' + meta.part_gcta_job
117+
[[ id:prefix ], grm_id, grm_bin, grm_n_bin]
118+
}
119+
120+
input[0] = dense_grm
121+
input[1] = Channel.value(0.05)
97122
"""
98123
}
99124
}
@@ -103,6 +128,10 @@ nextflow_process {
103128
when {
104129
process {
105130
"""
131+
sparse_grm = GCTA_MAKEBKSPARSE_DENSE.out.sparse_grm_files.map { meta, sparse_grm_id, sparse_grm_sp ->
132+
[[ id:meta.id + '_sp' ], sparse_grm_id, sparse_grm_sp]
133+
}
134+
106135
quantitative_pheno = GAWK_QUANTITATIVE_PHENO.out.output.map { meta, phenotype_file ->
107136
[[ id:meta.id, is_binary:false ], phenotype_file]
108137
}
@@ -113,7 +142,7 @@ nextflow_process {
113142
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.bim", checkIfExists: true),
114143
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.fam", checkIfExists: true)
115144
]
116-
input[1] = GCTA_TEST_PREPARE_SPARSE_DENSE.out.sparse_grm
145+
input[1] = sparse_grm
117146
input[2] = quantitative_pheno
118147
input[3] = GAWK_QUANTITATIVE_COVARIATES.out.output
119148
input[4] = GAWK_CATEGORICAL_COVARIATES.out.output
@@ -147,6 +176,10 @@ nextflow_process {
147176
when {
148177
process {
149178
"""
179+
sparse_grm = GCTA_MAKEBKSPARSE_DENSE.out.sparse_grm_files.map { meta, sparse_grm_id, sparse_grm_sp ->
180+
[[ id:meta.id + '_sp' ], sparse_grm_id, sparse_grm_sp]
181+
}
182+
150183
multi_pheno = GAWK_MULTI_PHENO.out.output.map { meta, phenotype_file ->
151184
[[ id:'QuantitativeTraitMpheno2', is_binary:false ], phenotype_file]
152185
}
@@ -157,7 +190,7 @@ nextflow_process {
157190
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.bim", checkIfExists: true),
158191
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.fam", checkIfExists: true)
159192
]
160-
input[1] = GCTA_TEST_PREPARE_SPARSE_DENSE.out.sparse_grm
193+
input[1] = sparse_grm
161194
input[2] = multi_pheno
162195
input[3] = GAWK_QUANTITATIVE_COVARIATES.out.output
163196
input[4] = GAWK_CATEGORICAL_COVARIATES.out.output
@@ -239,6 +272,10 @@ nextflow_process {
239272
when {
240273
process {
241274
"""
275+
sparse_grm = GCTA_MAKEBKSPARSE_DENSE.out.sparse_grm_files.map { meta, sparse_grm_id, sparse_grm_sp ->
276+
[[ id:meta.id + '_sp' ], sparse_grm_id, sparse_grm_sp]
277+
}
278+
242279
quantitative_pheno = GAWK_QUANTITATIVE_PHENO.out.output.map { meta, phenotype_file ->
243280
[[ id:meta.id, is_binary:false ], phenotype_file]
244281
}
@@ -249,7 +286,7 @@ nextflow_process {
249286
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.pvar", checkIfExists: true),
250287
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.psam", checkIfExists: true)
251288
]
252-
input[1] = GCTA_TEST_PREPARE_SPARSE_DENSE.out.sparse_grm
289+
input[1] = sparse_grm
253290
input[2] = quantitative_pheno
254291
input[3] = [[ id:'covariates_quant' ], []]
255292
input[4] = [[ id:'covariates_cat' ], []]
@@ -281,11 +318,15 @@ nextflow_process {
281318
when {
282319
process {
283320
"""
321+
sparse_grm = GCTA_MAKEBKSPARSE_DENSE.out.sparse_grm_files.map { meta, sparse_grm_id, sparse_grm_sp ->
322+
[[ id:meta.id + '_sp' ], sparse_grm_id, sparse_grm_sp]
323+
}
324+
284325
quantitative_pheno = GAWK_QUANTITATIVE_PHENO.out.output.map { meta, phenotype_file ->
285326
[[ id:meta.id, is_binary:false ], phenotype_file]
286327
}
287328

288-
sparse_grm_bad_prefix = GCTA_TEST_PREPARE_SPARSE_DENSE.out.sparse_grm.map { meta, sparse_grm_id, sparse_grm_sp ->
329+
sparse_grm_bad_prefix = sparse_grm.map { meta, sparse_grm_id, sparse_grm_sp ->
289330
[[ id:'incorrect_sparse_prefix' ], sparse_grm_id, sparse_grm_sp]
290331
}
291332

@@ -320,6 +361,10 @@ nextflow_process {
320361
when {
321362
process {
322363
"""
364+
sparse_grm = GCTA_MAKEBKSPARSE_DENSE.out.sparse_grm_files.map { meta, sparse_grm_id, sparse_grm_sp ->
365+
[[ id:meta.id + '_sp' ], sparse_grm_id, sparse_grm_sp]
366+
}
367+
323368
quantitative_pheno = GAWK_QUANTITATIVE_PHENO.out.output.map { meta, phenotype_file ->
324369
[[ id:meta.id, is_binary:false ], phenotype_file]
325370
}
@@ -330,7 +375,7 @@ nextflow_process {
330375
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.pvar", checkIfExists: true),
331376
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/plink_simulated.psam", checkIfExists: true)
332377
]
333-
input[1] = GCTA_TEST_PREPARE_SPARSE_DENSE.out.sparse_grm
378+
input[1] = sparse_grm
334379
input[2] = quantitative_pheno
335380
input[3] = [[ id:'covariates_quant' ], []]
336381
input[4] = [[ id:'covariates_cat' ], []]

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