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tests: use makegrmpart setup for gcta/addgrms
1 parent 9623225 commit c6d78e2

2 files changed

Lines changed: 37 additions & 61 deletions

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‎modules/nf-core/gcta/addgrms/tests/helpers/gcta_makegrm/main.nf‎

Lines changed: 0 additions & 38 deletions
This file was deleted.

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

Lines changed: 37 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -8,8 +8,8 @@ nextflow_process {
88
tag "modules_nfcore"
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tag "gcta"
1010
tag "gcta/addgrms"
11+
tag "gcta/makegrmpart"
1112
tag "gawk"
12-
tag "tests/helpers/gcta_makegrm"
1313

1414
setup {
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run("GAWK", alias: "GAWK_VARIANTS_LDMS1") {
@@ -40,36 +40,50 @@ nextflow_process {
4040
}
4141
}
4242

43-
run("GCTA_TEST_MAKEGRM", alias: "GCTA_TEST_MAKEGRM_LDMS1") {
44-
script "../tests/helpers/gcta_makegrm/main.nf"
43+
run("GCTA_MAKEGRMPART", alias: "GCTA_MAKEGRMPART_LDMS1") {
44+
script "../../makegrmpart/main.nf"
4545
process {
4646
"""
47-
input[0] = GAWK_VARIANTS_LDMS1.out.output.map { meta, ldms1_variants_file ->
47+
file('plink_simulated.mbfile').text = 'plink_simulated\\n'
48+
49+
input[0] = [
50+
[ id:'plink_simulated_ldms1', part_gcta_job:1, nparts_gcta:1 ],
51+
file('plink_simulated.mbfile'),
52+
[
53+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
54+
],
4855
[
49-
[ id:'plink_simulated_ldms1' ],
50-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
51-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
52-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true),
53-
ldms1_variants_file
56+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
57+
],
58+
[
59+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
5460
]
55-
}
61+
]
62+
input[1] = GAWK_VARIANTS_LDMS1.out.output
5663
"""
5764
}
5865
}
5966

60-
run("GCTA_TEST_MAKEGRM", alias: "GCTA_TEST_MAKEGRM_LDMS2") {
61-
script "../tests/helpers/gcta_makegrm/main.nf"
67+
run("GCTA_MAKEGRMPART", alias: "GCTA_MAKEGRMPART_LDMS2") {
68+
script "../../makegrmpart/main.nf"
6269
process {
6370
"""
64-
input[0] = GAWK_VARIANTS_LDMS2.out.output.map { meta, ldms2_variants_file ->
71+
file('plink_simulated.mbfile').text = 'plink_simulated\\n'
72+
73+
input[0] = [
74+
[ id:'plink_simulated_ldms2', part_gcta_job:1, nparts_gcta:1 ],
75+
file('plink_simulated.mbfile'),
76+
[
77+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
78+
],
6579
[
66-
[ id:'plink_simulated_ldms2' ],
67-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
68-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
69-
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true),
70-
ldms2_variants_file
80+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
81+
],
82+
[
83+
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
7184
]
72-
}
85+
]
86+
input[1] = GAWK_VARIANTS_LDMS2.out.output
7387
"""
7488
}
7589
}
@@ -85,8 +99,8 @@ nextflow_process {
8599
.of('plink_simulated_ldms1.part_1_1\\nplink_simulated_ldms2.part_1_1')
86100
.collectFile(name:'plink_simulated_ldms.mgrm', newLine: true)
87101

88-
grm_files = GCTA_TEST_MAKEGRM_LDMS1.out.grm_files
89-
.mix(GCTA_TEST_MAKEGRM_LDMS2.out.grm_files)
102+
grm_files = GCTA_MAKEGRMPART_LDMS1.out.grm_files
103+
.mix(GCTA_MAKEGRMPART_LDMS2.out.grm_files)
90104
.map { meta, grm_id, grm_bin, grm_n_bin -> [grm_id, grm_bin, grm_n_bin] }
91105
.collect()
92106
.map { rows -> rows.sort { left, right -> left[0].name <=> right[0].name }.flatten() }
@@ -125,8 +139,8 @@ nextflow_process {
125139
.of('plink_simulated_ldms1.part_1_1\\nplink_simulated_ldms2.part_1_1')
126140
.collectFile(name:'plink_simulated_ldms.mgrm', newLine: true)
127141

128-
grm_files = GCTA_TEST_MAKEGRM_LDMS1.out.grm_files
129-
.mix(GCTA_TEST_MAKEGRM_LDMS2.out.grm_files)
142+
grm_files = GCTA_MAKEGRMPART_LDMS1.out.grm_files
143+
.mix(GCTA_MAKEGRMPART_LDMS2.out.grm_files)
130144
.map { meta, grm_id, grm_bin, grm_n_bin -> [grm_id, grm_bin, grm_n_bin] }
131145
.collect()
132146
.map { rows -> rows.sort { left, right -> left[0].name <=> right[0].name }.flatten() }

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