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

Include nf-tests for rsem_merge_counts module #1249

Merged
merged 10 commits into from
Mar 12, 2024
Merged

Include nf-tests for rsem_merge_counts module #1249

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
6f5632c
Initial attempt at nf-test for rsem_merge_counts
robsyme Mar 9, 2024
e71d687
Include test data
robsyme Mar 9, 2024
0ad06dc
Update modules/local/rsem_merge_counts/tests/main.nf.test
maxulysse Mar 11, 2024
6e5c91d
data to github
maxulysse Mar 11, 2024
089d9af
fix path
maxulysse Mar 11, 2024
5af2b1d
Merge branch 'dev' into nftest_rsem_merge_counts
maxulysse Mar 12, 2024
5ac549f
collect input files
maxulysse Mar 12, 2024
0f90900
Update modules/local/rsem_merge_counts/tests/main.nf.test
maxulysse Mar 12, 2024
be63894
forgot to commit this file deletion
maxulysse Mar 12, 2024
49d8fff
Update modules/local/rsem_merge_counts/tests/main.nf.test
maxulysse Mar 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
33 changes: 33 additions & 0 deletions modules/local/rsem_merge_counts/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
nextflow_process {

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

test("Should run without failures") {

when {
process {
"""
input[0] = Channel.of([
file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_IAA_30M_REP1.genes.results", checkIfExists: true),
file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP1.genes.results", checkIfExists: true),
file(params.pipelines_testdata_base_path + "rsem_merge_counts/genes/RAP1_UNINDUCED_REP2.genes.results", checkIfExists: true)
]).collect()
input[1] = Channel.of([
file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_IAA_30M_REP1.isoforms.results", checkIfExists: true),
file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP1.isoforms.results", checkIfExists: true),
file(params.pipelines_testdata_base_path + "rsem_merge_counts/isoforms/RAP1_UNINDUCED_REP2.isoforms.results", checkIfExists: true)
]).collect()
"""
}
}

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

}

}
43 changes: 43 additions & 0 deletions modules/local/rsem_merge_counts/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
{
"Should run without failures": {
"content": [
{
"0": [
"rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446"
],
"1": [
"rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
],
"2": [
"rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
],
"3": [
"rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
],
"4": [
"versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
],
"counts_gene": [
"rsem.merged.gene_counts.tsv:md5,7d1da94077dc2f90cfb2c793ca5b7446"
],
"counts_transcript": [
"rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
],
"tpm_gene": [
"rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
],
"tpm_transcript": [
"rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
],
"versions": [
"versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-09T17:13:37.377348"
}
}
Loading