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Merged
SPPearce merged 1 commit into from
May 21, 2026
+33 −114
Merged

Update test for hicap #11708

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16 changes: 8 additions & 8 deletions modules/nf-core/hicap/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process HICAP {
tuple val(meta), path("*.gbk"), emit: gbk, optional: true
tuple val(meta), path("*.svg"), emit: svg, optional: true
tuple val(meta), path("*.tsv"), emit: tsv, optional: true
tuple val("${task.process}"), val('hicap'), eval('hicap --version 2>&1 | sed \'s/^.*hicap //\''), emit: versions_hicap, topic: versions
tuple val("${task.process}"), val('hicap'), eval("hicap --version 2>&1 | sed 's/^.*hicap //'"), emit: versions_hicap, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -28,15 +28,15 @@ process HICAP {
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
def fasta_name = fasta.getName().replace(".gz", "")
"""
if [ "$is_compressed" == "true" ]; then
gzip -c -d $fasta > $fasta_name
if [ "${is_compressed}" == "true" ]; then
gzip -c -d $fasta > ${fasta_name}
fi
hicap \\
--query_fp $fasta_name \\
$database_args \\
$model_args \\
$args \\
--threads $task.cpus \\
--query_fp ${fasta_name} \\
${database_args} \\
${model_args} \\
${args} \\
--threads ${task.cpus} \\
-o ./
"""

Expand Down
14 changes: 3 additions & 11 deletions modules/nf-core/hicap/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,26 +14,19 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ],
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)
]
input[1] = []
input[2] = []

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.gbk[0][1]).readLines()[3..7],
file(process.out.svg[0][1]).readLines()[3..7],
process.out.tsv,
process.out.findAll { key, val -> key.startsWith('versions') }
).match()
}
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -45,12 +38,11 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ],
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)
]
input[1] = []
input[2] = []

"""
}
}
Expand Down
117 changes: 22 additions & 95 deletions modules/nf-core/hicap/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,73 +1,29 @@
{
"test-hicap": {
"content": [
[
"VERSION <unknown",
"KEYWORDS .",
"SOURCE .",
" ORGANISM .",
" ."
],
[
"\t<ns0:clipPath id=\"clip\">",
"\t\t<ns0:rect height=\"150\" width=\"1800\" x=\"0\" y=\"0\" />",
"\t</ns0:clipPath>",
"\t<ns0:g id=\"group\" style=\"clip-path: url(#clip)\" transform=\"scale(1,-1) translate(0,-150)\">",
"\t\t<ns0:g transform=\"\">"
],
[
[
{
"id": "test",
"single_end": false
},
"genome.tsv:md5,cd148cbec8c707e9c732c417a0e93d3b"
]
],
{
"versions_hicap": [
[
"HICAP",
"hicap",
"1.0.3"
]
]
}
],
"timestamp": "2026-05-18T22:23:36.468425818",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.2"
}
},
"test-hicap - stub": {
"content": [
{
"gbk": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e"
"genome.gbk:md5,562d026956903354ac80721f501335d4"
]
],
"svg": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"genome.svg:md5,d41d8cd98f00b204e9800998ecf8427e"
"genome.svg:md5,4fb94871dd0fdd8b4496049668176631"
]
],
"tsv": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"genome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
"genome.tsv:md5,cd148cbec8c707e9c732c417a0e93d3b"
]
],
"versions_hicap": [
Expand All @@ -79,81 +35,52 @@
]
}
],
"timestamp": "2026-05-18T22:23:41.930816628",
"timestamp": "2026-05-19T17:33:39.043348035",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.2"
"nextflow": "26.04.0"
}
},
"test-hicap-stub": {
"test-hicap - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"genome.svg:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"genome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
"versions.yml:md5,8f155331d348220ce0f7d6467340608a"
],
"gbk": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"svg": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"genome.svg:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"tsv": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"genome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,8f155331d348220ce0f7d6467340608a"
"versions_hicap": [
[
"HICAP",
"hicap",
"1.0.3"
]
]
}
],
"timestamp": "2024-08-30T19:25:16.144267",
"timestamp": "2026-05-19T17:33:47.557759254",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
}
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