8000 srst2/srst2 to nf-test by famosab · Pull Request #8301 · nf-core/modules · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

srst2/srst2 to nf-test #8301

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 9 commits into from
May 28, 2025
Merged

srst2/srst2 to nf-test #8301

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
bbc9b69
srst2/srst2 to nf-test
famosab Apr 14, 2025
2bb2181
samtools error :(
famosab Apr 14, 2025
5f35cdd
Merge branch 'master' into srst
famosab Apr 15, 2025
4932d7f
Merge branch 'master' into srst
famosab May 16, 2025
35d443d
update
famosab May 16, 2025
60249c8
Merge branch 'master' into srst
maxulysse May 19, 2025
c9bbcf3
Merge branch 'master' into srst
famosab May 28, 2025
5351d5c
move db to val input channel
famosab May 28, 2025
e8c3609
Merge branch 'master' into srst
famosab May 28, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
43 changes: 33 additions & 10 deletions modules/nf-core/srst2/srst2/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,14 +9,15 @@ process SRST2_SRST2 {

input:
tuple val(meta), path(fastq_s), path(db)
val(db_type)

output:
tuple val(meta), path("*_genes_*_results.txt") , optional:true, emit: gene_results
tuple val(meta), path("*_fullgenes_*_results.txt") , optional:true, emit: fullgene_results
tuple val(meta), path("*_mlst_*_results.txt") , optional:true, emit: mlst_results
tuple val(meta), path("*.pileup") , emit: pileup
tuple val(meta), path("*.sorted.bam") , emit: sorted_bam
path "versions.yml" , emit: versions
tuple val(meta), path("*_genes_*_results.txt") , emit: gene_results , optional:true
tuple val(meta), path("*_fullgenes_*_results.txt"), emit: fullgene_results, optional:true
tuple val(meta), path("*_mlst_*_results.txt") , emit: mlst_results , optional:true
tuple val(meta), path("*.pileup") , emit: pileup
tuple val(meta), path("*.sorted.bam") , emit: sorted_bam
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -25,12 +26,12 @@ process SRST2_SRST2 {
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def read_s = meta.single_end ? "--input_se ${fastq_s}" : "--input_pe ${fastq_s[0]} ${fastq_s[1]}"
if (meta.db=="gene") {
if (db_type=="gene") {
database = "--gene_db ${db}"
} else if (meta.db=="mlst") {
} else if (db_type=="mlst") {
database = "--mlst_db ${db}"
} else {
error "Please set meta.db to either \"gene\" or \"mlst\""
error "Please set input[1] to either \"gene\" or \"mlst\""
}
"""
srst2 \\
Expand All @@ -39,9 +40,31 @@ process SRST2_SRST2 {
--output ${prefix} \\
${database} \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def db_name = db.getBaseName()
if (db_type=="gene") {
db_cmd = "touch ${prefix}__genes__${db_name}__results.txt ${prefix}__fullgenes__${db_name}__results.txt"
} else if (db_type=="mlst") {
db_cmd = "touch ${prefix}__mlst__${db_name}__results.txt"
} else {
error "Please set input[1] to either \"gene\" or \"mlst\""
}
"""
touch ${prefix}.pileup
touch ${prefix}.sorted.bam
${db_cmd}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' ))
srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' )
END_VERSIONS
"""
}
3 changes: 3 additions & 0 deletions modules/nf-core/srst2/srst2/meta.yml
View file
Open in desktop
10000
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,9 @@ input:
type: file
description: Database in FASTA format
pattern: "*.fasta"
- - db_type:
type: string
description: Type of database to use, either 'gene' or 'mlst'
output:
- gene_results:
- meta:
Expand Down
158 changes: 158 additions & 0 deletions modules/nf-core/srst2/srst2/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,158 @@
nextflow_process {

name "Test Process SRST2_SRST2"

script "../main.nf"
process "SRST2_SRST2"

tag "modules"
tag "modules_nfcore"
tag "srst2"
tag "srst2/srst2"

test("delete_me - fastq.gz") {

when {
process {
"""
input[0] = [
[id:'test', single_end:false],// meta map
[
file(params.modules_testdata_base_path + 'delete_me/srst2/SRR9067271_1.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'delete_me/srst2/SRR9067271_2.fastq.gz',checkIfExists:true)
],
file(params.modules_testdata_base_path + 'delete_me/srst2/MLST_DB.fas', checkIfExists:true)
]
input[1] = "mlst"
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
path(process.out.mlst_results.get(0).get(1)).readLines(),
path(process.out.pileup.get(0).get(1)).readLines()[0..10],
bam(process.out.sorted_bam.get(0).get(1)).getStatistics(),
process.out.versions
).match() }
)
}
}

// test("bacteroides_fragilis - fastq.gz - paired_end") {

// when {
// process {
// """
// input[0] = [
// [id:'test', single_end:false],// meta map
// [
// file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz',checkIfExists:true),
// file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz',checkIfExists:true)
// ],
// file(params.modules_testdata_base_path + 'delete_me/srst2/resFinder_20180221_srst2.fasta',checkIfExists:true)
// ]
// input[1] = "gene"
// """
// }
// }
// then {
// assertAll(
// { assert process.success },
// { assert snapshot(
// path(process.out.gene_results.get(0).get(1)).readLines(),
// path(process.out.fullgene_results.get(0).get(1)).readLines(),
// path(process.out.pileup.get(0).get(1)).readLines(),
// bam(process.out.sorted_bam.get(0).get(1)).getReadsMD5(),
// process.out.versions
// ).match() }
// )
// }
// }

// test("bacteroides_fragilis - fastq.gz - single_end") {

// when {
// process {
// """
// input[0] = [
// [id:'test', single_end:true],// meta map
// file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists:true),
// file(params.modules_testdata_base_path + 'delete_me/srst2/resFinder_20180221_srst2.fasta', checkIfExists:true)
// ]
// input[1] = "gene"
// """
// }
// }
// then {
// assertAll(
// { assert process.success },
// { assert snapshot(
// path(process.out.gene_results.get(0).get(1)).readLines(),
// path(process.out.fullgene_results.get(0).get(1)).readLines(),
// path(process.out.pileup.get(0).get(1)).readLines(),
// bam(process.out.sorted_bam.get(0).get(1)).getReadsMD5(),
// process.out.versions
// ).match() }
// )
// }
// }

test("delete_me - fastq.gz - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[id:'test', single_end:false],// meta map
[
file(params.modules_testdata_base_path + 'delete_me/srst2/SRR9067271_1.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'delete_me/srst2/SRR9067271_2.fastq.gz',checkIfExists:true)
],
file(params.modules_testdata_base_path + 'delete_me/srst2/MLST_DB.fas', checkIfExists:true)
]
input[1] = "mlst"
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}
}

test("bacteroides_fragilis - fastq.gz - single_end - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[id:'test',single_end:true],// meta map
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'delete_me/srst2/resFinder_20180221_srst2.fasta',checkIfExists:true)
]
input[1] = "gene"
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}
}
}
Loading
Loading
0