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

add nf-test tests and snapshots #323

Closed
wants to merge 14 commits into from
Closed

add nf-test tests and snapshots #323

Changes from 1 commit
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
274042b
Merge pull request #316 from nf-core/dev
jasmezz Nov 7, 2023
b906a38
first nf-test with snapshot
Nov 14, 2023
8c0f220
update test.nf.test and snapshot
Nov 17, 2023
9f4cb6f
fixed path in nf-test.config
Nov 17, 2023
d614e3f
add test_bgc.nf.test and snapshot
Nov 17, 2023
d4b1c8d
update CHANGELOG
Nov 17, 2023
04539ac
Merge branch 'dev' into nftest
louperelo Nov 20, 2023
82e11c3
[automated] Fix linting with Prettier
nf-core-bot Nov 20, 2023
6e841d7
Merge branch 'nf-core:master' into nftest
louperelo Nov 20, 2023
abf2f14
add test_deeparg.nf.test and snapshot
Nov 20, 2023
23c2be4
nf.test and snapshot for whole pipeline test
Nov 21, 2023
0c8e7c1
fix formatting
Nov 21, 2023
1171c90
fix formatting
Nov 21, 2023
274f10b
Fix tag
jfy133 Jan 24, 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
Prev Previous commit
Next Next commit
fix formatting
louperelo committed Nov 21, 2023
commit 0c8e7c1fdcf44c109a0102f6e9beee1139844279
2 changes: 1 addition & 1 deletion tests/lib/UTILS.groovy
View file
Original file line number Diff line number Diff line change
@@ -35,4 +35,4 @@ class UTILS {
return outputFile
}
}
}
}
4 changes: 2 additions & 2 deletions tests/pipeline/test.nf.test
View file
Original file line number Diff line number Diff line change
@@ -27,7 +27,7 @@ nextflow_pipeline {
{ assert new File("$outputDir/amp/macrel/sample_1/sample_1.prediction.gz").exists() },
{ assert snapshot(path("$outputDir/amp/macrel/sample_2/sample_2_log.txt"),
path("$outputDir/amp/macrel/sample_2/README.md")).match("amp_macrel_sample_2") },
{ assert new File("$outputDir/amp/macrel/sample_2/sample_2.all_orfs.faa.gz").exists() },
{ assert new File("$outputDir/amp/macrel/sample_2/sample_2.all_orfs.faa.gz").exists() },
{ assert new File("$outputDir/amp/macrel/sample_2/sample_2.prediction.gz").exists() },
{ assert snapshot(path("$outputDir/arg/abricate/").list()).match("arg_abricate") },
{ assert snapshot(path("$outputDir/arg/amrfinderplus/").list()).match("arg_amrfinderplus") },
@@ -53,7 +53,7 @@ nextflow_pipeline {
{ assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_amp.faa").exists() },
{ assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_ampcombi.csv").exists() },
{ assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_diamond_matches.txt").exists() },
{ assert snapshot(path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv")).match("summary_hamronization") }
{ assert snapshot(path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv")).match("summary_hamronization") }
)
}

34 changes: 17 additions & 17 deletions tests/pipeline/test_all.nf.test
View file
Original file line number Diff line number Diff line change
@@ -22,7 +22,7 @@ nextflow_pipeline {
run_bgc_screening = true
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv'
}

}

then {
@@ -39,7 +39,7 @@ nextflow_pipeline {
{ assert new File("$outputDir/amp/macrel/sample_1/sample_1.prediction.gz").exists() },
{ assert snapshot(path("$outputDir/amp/macrel/sample_2/sample_2_log.txt"),
path("$outputDir/amp/macrel/sample_2/README.md")).match("amp_macrel_sample_2") },
{ assert new File("$outputDir/amp/macrel/sample_2/sample_2.all_orfs.faa.gz").exists() },
{ assert new File("$outputDir/amp/macrel/sample_2/sample_2.all_orfs.faa.gz").exists() },
{ assert new File("$outputDir/amp/macrel/sample_2/sample_2.prediction.gz").exists() },
{ assert snapshot(path("$outputDir/arg/abricate/").list()).match("arg_abricate") },
{ assert snapshot(path("$outputDir/arg/amrfinderplus/").list()).match("arg_amrfinderplus") },
@@ -79,21 +79,21 @@ nextflow_pipeline {
{ assert snapshot(path("$outputDir/bgc/antismash/sample_2/css").list()).match("bgc_antismash_css") },
{ assert snapshot(path("$outputDir/bgc/antismash/sample_2/images").list()).match("bgc_antismash_images") },
{ assert snapshot(path("$outputDir/bgc/deepbgc/sample_1/README.txt"),
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.score.png"),
path("$outputDir/bgc/deepbgc/sample_2/README.txt"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.score.png")).match("bgc_deepbgc") },
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.score.png"),
path("$outputDir/bgc/deepbgc/sample_2/README.txt"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.score.png")).match("bgc_deepbgc") },
{ assert snapshot(path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.clusters.tsv"),
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.features.tsv"),
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.genes.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.clusters.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.features.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.genes.tsv"),).match("bgc_gecco") },
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.features.tsv"),
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.genes.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.clusters.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.features.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.genes.tsv"),).match("bgc_gecco") },
{ assert snapshot(path("$outputDir/arg/hamronization/").list()).match("arg_hamronization") },
{ assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt")).match("multiqc") },
@@ -105,7 +105,7 @@ nextflow_pipeline {
{ assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_ampcombi.csv").exists() },
{ assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_diamond_matches.txt").exists() },
{ assert snapshot(path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv")).match("summary_hamronization") },
{ assert new File("$outputDir/reports/combgc/combgc_complete_summary.tsv").exists() }
{ assert new File("$outputDir/reports/combgc/combgc_complete_summary.tsv").exists() }
)
}

30 changes: 14 additions & 16 deletions tests/pipeline/test_bgc.nf.test
View file
Original file line number Diff line number Diff line change
@@ -25,7 +25,6 @@ nextflow_pipeline {
{ assert new File("$outputDir/bgc/antismash/sample_1/wastewater_metagenome_contigs_1.json").exists() },
{ assert snapshot(path("$outputDir/bgc/antismash/sample_1/css").list()).match("bgc_antismash_css") },
{ assert snapshot(path("$outputDir/bgc/antismash/sample_1/images").list()).match("bgc_antismash_images") },

{ assert new File("$outputDir/bgc/antismash/sample_2/NODE_6_length_23263_cov_4.891675.region001.gbk").exists() },
{ assert new File("$outputDir/bgc/antismash/sample_2/NODE_5815_length_1804_cov_1.983419.region001.gbk").exists() },
{ assert new File("$outputDir/bgc/antismash/sample_2/NODE_21026_length_1024_cov_1.925697.region001.gbk").exists() },
@@ -35,23 +34,22 @@ nextflow_pipeline {
{ assert snapshot(path("$outputDir/bgc/antismash/sample_2/css").list()).match("bgc_antismash_css") },
{ assert snapshot(path("$outputDir/bgc/antismash/sample_2/images").list()).match("bgc_antismash_images") },
{ assert snapshot(path("$outputDir/bgc/deepbgc/sample_1/README.txt"),
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.score.png"),
path("$outputDir/bgc/deepbgc/sample_2/README.txt"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.score.png")).match("bgc_deepbgc") },
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_1/wastewater_metagenome_contigs_1.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_1/evaluation/wastewater_metagenome_contigs_1.score.png"),
path("$outputDir/bgc/deepbgc/sample_2/README.txt"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.bgc.gbk"),
path("$outputDir/bgc/deepbgc/sample_2/wastewater_metagenome_contigs_2.pfam.tsv"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.bgc.png"),
path("$outputDir/bgc/deepbgc/sample_2/evaluation/wastewater_metagenome_contigs_2.score.png")).match("bgc_deepbgc") },
{ assert snapshot(path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.clusters.tsv"),
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.features.tsv"),
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.genes.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.clusters.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.features.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.genes.tsv"),).match("bgc_gecco") },
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.features.tsv"),
path("$outputDir/bgc/gecco/sample_1/wastewater_metagenome_contigs_1.genes.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.clusters.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.features.tsv"),
path("$outputDir/bgc/gecco/sample_2/wastewater_metagenome_contigs_2.genes.tsv"),).match("bgc_gecco") },
{ assert new File("$outputDir/reports/combgc/combgc_complete_summary.tsv").exists() },

)
}