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ltrretriever/ltrretriever: Added test to verify graceful handling of … (
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#5980)

* ltrretriever/ltrretriever: Added test to verify graceful handling of no ltr input

* Removed unstable items from snapshot
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@GallVp
GallVp authored Jul 20, 2024
1 parent be4f907 commit 35787cd
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Showing 5 changed files with 99 additions and 68 deletions.
15 changes: 8 additions & 7 deletions modules/nf-core/ltrretriever/ltrretriever/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,9 @@ process LTRRETRIEVER_LTRRETRIEVER {

output:
tuple val(meta), path("*.log") , emit: log
tuple val(meta), path("${prefix}.pass.list"), emit: pass_list
tuple val(meta), path("*.pass.list.gff3") , emit: pass_list_gff
tuple val(meta), path("*.LTRlib.fa") , emit: ltrlib
tuple val(meta), path("${prefix}.pass.list"), emit: pass_list , optional: true
tuple val(meta), path("*.pass.list.gff3") , emit: pass_list_gff , optional: true
tuple val(meta), path("*.LTRlib.fa") , emit: ltrlib , optional: true
tuple val(meta), path("${prefix}.out") , emit: annotation_out , optional: true
tuple val(meta), path("*.out.gff3") , emit: annotation_gff , optional: true
path "versions.yml" , emit: versions
Expand All @@ -42,11 +42,12 @@ process LTRRETRIEVER_LTRRETRIEVER {
$non_tgca_file \\
-threads $task.cpus \\
$args \\
&> >(tee "${prefix}.log" 2>&1)
&> >(tee "${prefix}.log" 2>&1) \\
|| echo "Errors from LTR_retriever printed to ${prefix}.log"
mv "${genome}.pass.list" "${prefix}.pass.list"
mv "${genome}.pass.list.gff3" "${prefix}.pass.list.gff3"
mv "${genome}.LTRlib.fa" "${prefix}.LTRlib.fa"
mv "${genome}.pass.list" "${prefix}.pass.list" || echo ".pass.list was not produced"
mv "${genome}.pass.list.gff3" "${prefix}.pass.list.gff3" || echo ".pass.list.gff3 was not produced"
mv "${genome}.LTRlib.fa" "${prefix}.LTRlib.fa" || echo ".LTRlib.fa was not produced"
mv "${genome}.out" "${prefix}.out" || echo ".out was not produced"
mv "${genome}.out.gff3" "${prefix}.out.gff3" || echo ".out.gff3 was not produced"
Expand Down
91 changes: 72 additions & 19 deletions modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,45 +10,99 @@ nextflow_process {
tag "ltrretriever"
tag "ltrretriever/ltrretriever"
tag "gunzip/main"
tag "gt/ltrharvest"
tag "gt/suffixerator"
tag "ltrharvest"
tag "ltrfinder"
tag "cat/cat"

test("actinidia_chinensis-genome_21_fasta_gz-success") {
test("sarscov2-genome-no_ltr") {

setup {

run('GUNZIP') {
script "../../../gunzip/main"
run("LTRHARVEST") {
script "../../../ltrharvest"

process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
"""
}
}

run("GT_SUFFIXERATOR") {
script "../../../gt/suffixerator"
run("LTRFINDER") {
script "../../../ltrfinder"

process {
"""
input[0] = GUNZIP.out.gunzip
input[1] = 'dna'
input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
"""
}
}

run("CAT_CAT") {
script "../../../cat/cat"

process {
"""
input[0] = LTRHARVEST.out.scn.mix(LTRFINDER.out.scn).groupTuple()
"""
}
}
}

when {
process {
"""
input[0] = input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = CAT_CAT.out.file_out.map { meta, tabout -> tabout }
input[2] = []
input[3] = []
input[4] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.log[0][1]).text.contains("ERROR: No candidate is found in the file(s) you specified.") },
{ assert snapshot(process.out.versions).match("versions_no_ltr") }
)
}

}

test("actinidia_chinensis-genome_21_fasta_gz-success") {

setup {

run('GUNZIP') {
script "../../../gunzip/main"

process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true)
]
"""
}
}

run("GT_LTRHARVEST") {
script "../../../gt/ltrharvest"
run("LTRHARVEST") {
script "../../../ltrharvest"

process {
"""
input[0] = GT_SUFFIXERATOR.out.index
input[0] = GUNZIP.out.gunzip
"""
}
}
Expand All @@ -68,7 +122,7 @@ nextflow_process {

process {
"""
input[0] = GT_LTRHARVEST.out.tabout.mix(LTRFINDER.out.scn).groupTuple()
input[0] = LTRHARVEST.out.scn.mix(LTRFINDER.out.scn).groupTuple()
"""
}
}
Expand All @@ -90,7 +144,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert path(process.out.log[0][1]).text.contains("####### Result files #########") },
{ assert snapshot(process.out.pass_list).match("pass_list") },
{ assert path(process.out.pass_list[0][1]).text.contains("Copia\tLTR") },
{ assert path(process.out.pass_list_gff[0][1]).text.contains("chr1\tLTR_retriever\ttarget_site_duplication") },
{ assert path(process.out.ltrlib[0][1]).text.contains("LTR#LTR/Copia") },
{ assert snapshot(process.out.annotation_out).match("annotation_out") },
Expand All @@ -110,7 +164,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true)
]
input[1] = []
input[2] = []
Expand All @@ -123,8 +177,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(path(process.out.versions[0]).text).match("versions_stub") }
{ assert snapshot(process.out).match() }
)
}

Expand Down
47 changes: 16 additions & 31 deletions modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,31 +1,4 @@
{
"versions_stub": {
"content": [
"\"LTRRETRIEVER_LTRRETRIEVER\":\n LTR_retriever: v2.9.9\n"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-02-19T11:04:16.007262"
},
"pass_list": {
"content": [
[
[
{
"id": "test"
},
"test.pass.list:md5,0c96ee3b48691e65da2235786a926160"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-02-19T11:17:50.087449"
},
"versions": {
"content": [
"\"LTRRETRIEVER_LTRRETRIEVER\":\n LTR_retriever: v2.9.9\n"
Expand Down Expand Up @@ -156,14 +129,26 @@
{
"id": "test"
},
"test.out:md5,4ecf9226cbd7a3aaf7cf5cfa575fcc6a"
"test.out:md5,33d89bea9031f25de8f0d3591ab94d87"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-07-16T14:18:02.458476"
},
"versions_no_ltr": {
"content": [
[
"versions.yml:md5,3ab159acaee06b342b56e2d35e5e669b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-02-19T11:17:50.150622"
"timestamp": "2024-07-16T14:03:52.324194"
}
}
}
12 changes: 3 additions & 9 deletions modules/nf-core/ltrretriever/ltrretriever/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,18 +1,12 @@
process {

withName: GT_SUFFIXERATOR {
ext.args = '-suf -lcp'
// GT_LTRHARVEST requires -suf, -lcp
}

withName: LTRFINDER {
ext.args = '-harvest_out'
// LTRRETRIEVER requires -harvest_out
// LTRRETRIEVER_LTRRETRIEVER requires -harvest_out
}

withName: GT_LTRHARVEST {
ext.args = '-minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 -seqids yes'
// recommended parameters: https://github.com/oushujun/LTR_retriever#usage
withName: LTRHARVEST {
ext.prefix = { "${meta.id}_ltrharvest" }
}

withName: CAT_CAT {
Expand Down
2 changes: 0 additions & 2 deletions modules/nf-core/ltrretriever/ltrretriever/tests/tags.yml
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