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

CHORES: Update STRINGTIE module to use path rather than map #4879

Merged
merged 4 commits into from
Feb 12, 2024
Merged

CHORES: Update STRINGTIE module to use path rather than map #4879

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
7335cee
CHORES: Update STRINGTIE module to use path rather than map
adamrtalbot Feb 7, 2024
b942d30
update stringtie tests
adamrtalbot Feb 7, 2024
98367dd
Update modules/nf-core/stringtie/merge/tests/main.nf.test
maxulysse Feb 12, 2024
d552ec2
Merge branch 'master' into stringtie_update_paths
maxulysse Feb 12, 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
Next Next commit
CHORES: Update STRINGTIE module to use path rather than map
  • Loading branch information
@adamrtalbot
adamrtalbot committed Feb 7, 2024
commit 7335ceec1144c0ec75bdd98004f22b8679293f87
45 changes: 14 additions & 31 deletions modules/nf-core/stringtie/merge/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,23 +8,22 @@ nextflow_process {
tag "stringtie"
tag "stringtie/merge"
maxulysse marked this conversation as resolved.
Show resolved Hide resolved

test("homo_sapiens - forward strandedness") {

setup {
run("STRINGTIE_STRINGTIE") {
script "../../stringtie/main.nf"
process {
"""
input[0] = [
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
"""
}
setup {
run("STRINGTIE_STRINGTIE") {
script "../../stringtie/main.nf"
process {
"""
input[0] = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
]
input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
"""
}

}
}

test("homo_sapiens - forward strandedness") {

when {
process {
Expand All @@ -46,22 +45,6 @@ nextflow_process {

test("homo_sapiens - reverse strandedness") {

setup {
run("STRINGTIE_STRINGTIE") {
script "../../stringtie/main.nf"
process {
"""
input[0] = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
"""
}
}

}

when {
process {
"""
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/stringtie/stringtie/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
[ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
]
input[1] = []
"""
Expand All @@ -38,10 +38,10 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
]
input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
[ id:'test', strandedness:'forward' ], // meta map
[ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
]
input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
"""
}
}
Expand All @@ -64,7 +64,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
[ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
]
input[1] = []
"""
Expand All @@ -88,9 +88,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test', strandedness:'reverse' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
[ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
]
input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
"""
}
}
Expand Down
Loading