Skip to content
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

Jump to bottom

nf-test for pilon #5293

Merged
merged 9 commits into from
Jun 27, 2024
Merged

nf-test for pilon #5293

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
7c61023
nf-test for pilon
thanhleviet Mar 19, 2024
ba50ec6
linting for license
thanhleviet Mar 19, 2024
f23a68c
Add stub and extra test
SPPearce Jun 14, 2024
e3e0e8a
Merge branch 'master' into nf-test-pilon
SPPearce Jun 14, 2024
cc13531
Swap to testdata_base_path
SPPearce Jun 14, 2024
8b32825
Add missing END_VERSIONS and alignment
SPPearce Jun 22, 2024
0d30c4b
Merge branch 'master' into nf-test-pilon
SPPearce Jun 26, 2024
9fc40f3
Add optional outputs to stub
SPPearce Jun 27, 2024
16dd9c8
Merge branch 'master' into nf-test-pilon
SPPearce Jun 27, 2024
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
25 changes: 22 additions & 3 deletions modules/nf-core/pilon/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ process PILON {

input:
tuple val(meta), path(fasta)
tuple val(meta_bam), path(bam), path(bai)
tuple val(meta2), path(bam), path(bai)
val pilon_mode

output:
Expand All @@ -24,8 +24,8 @@ process PILON {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def valid_mode = ["frags", "jumps", "unpaired", "bam"]
if ( !valid_mode.contains(pilon_mode) ) { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
"""
Expand All @@ -39,5 +39,24 @@ process PILON {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
SPPearce marked this conversation as resolved.
Show resolved Hide resolved
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def valid_mode = ["frags", "jumps", "unpaired", "bam"]
SPPearce marked this conversation as resolved.
Show resolved Hide resolved
if ( !valid_mode.contains(pilon_mode) ) { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
"""
touch ${prefix}.fasta
SPPearce marked this conversation as resolved.
Show resolved Hide resolved
touch ${prefix}.vcf
touch ${prefix}.change
touch ${prefix}.bed
touch ${prefix}.wig

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
SPPearce marked this conversation as resolved.
Show resolved Hide resolved
END_VERSIONS
"""

}
9 changes: 7 additions & 2 deletions modules/nf-core/pilon/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,22 @@ tools:
documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage"
tool_dev_url: "https://github.com/broadinstitute/pilon"
doi: "10.1371/journal.pone.0112963"
licence: "['GPL v2']"
licence: ["GPL-2.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
Groovy Map containing sample information for the fasta
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA of the input genome
pattern: "*.{fasta}"
- meta2:
type: map
description: |
Groovy Map containing sample information for the bam file
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file of reads aligned to the input genome
Expand Down
116 changes: 116 additions & 0 deletions modules/nf-core/pilon/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,116 @@
nextflow_process {

name "Test Process PILON"
script "../main.nf"
process "PILON"

tag "modules"
tag "modules_nfcore"
tag "pilon"


test("homo sapiens bam") {

when {
process {
"""
input[0] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
]
input[1] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
]
input[2] = "bam"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}
SPPearce marked this conversation as resolved.
Show resolved Hide resolved

test("homo sapiens bam - stub") {
options "-stub"
when {
process {
"""
input[0] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
]
input[1] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
]
input[2] = "bam"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("homo sapiens frags") {

when {
process {
"""
input[0] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
]
input[1] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
]
input[2] = "frags"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("homo sapiens frags - stub") {
options "-stub"
when {
process {
"""
input[0] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
]
input[1] = [ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
]
input[2] = "frags"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

}
Loading
Loading