From 61c5dcc58ac534b07053d5873a622d315b4c6109 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:29:47 +0100 Subject: [PATCH 1/7] Add nf-test for STAR-RSEM and HISAT2 aligners --- CHANGELOG.md | 1 + tests/hisat2.main.nf.test | 22 ++++++++++++++++++++++ tests/star_rsem.main.nf.test | 22 ++++++++++++++++++++++ 3 files changed, 45 insertions(+) create mode 100644 tests/hisat2.main.nf.test create mode 100644 tests/star_rsem.main.nf.test diff --git a/CHANGELOG.md b/CHANGELOG.md index 651d6fe8c..91336a5e7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -80,6 +80,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes - [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison - [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file +- [PR #####]() - Add pipeline level test for STAR-RSEM and HISAT2 ### Parameters diff --git a/tests/hisat2.main.nf.test b/tests/hisat2.main.nf.test new file mode 100644 index 000000000..5b1e77130 --- /dev/null +++ b/tests/hisat2.main.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline with HISAT2 aligner" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("Default profile test") { + + when { + params { + outdir = "$outputDir" + aligner = 'hisat2' + } + } + + then { + assert workflow.success + } + } +} + diff --git a/tests/star_rsem.main.nf.test b/tests/star_rsem.main.nf.test new file mode 100644 index 000000000..b62897b0d --- /dev/null +++ b/tests/star_rsem.main.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline with STAR aligner and RSEM for quantification" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("Default profile test") { + + when { + params { + outdir = "$outputDir" + aligner = 'star_rsem' + } + } + + then { + assert workflow.success + } + } +} + From fa40d2066648eb01fbc1cde0eff5e10eeceab659 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:31:00 +0100 Subject: [PATCH 2/7] remove tags --- tests/hisat2.main.nf.test | 2 -- tests/star_rsem.main.nf.test | 2 -- 2 files changed, 4 deletions(-) diff --git a/tests/hisat2.main.nf.test b/tests/hisat2.main.nf.test index 5b1e77130..a20302422 100644 --- a/tests/hisat2.main.nf.test +++ b/tests/hisat2.main.nf.test @@ -2,8 +2,6 @@ nextflow_pipeline { name "Test pipeline with HISAT2 aligner" script "../main.nf" - tag "rnaseq" - tag "PIPELINE" test("Default profile test") { diff --git a/tests/star_rsem.main.nf.test b/tests/star_rsem.main.nf.test index b62897b0d..75e0f9f1b 100644 --- a/tests/star_rsem.main.nf.test +++ b/tests/star_rsem.main.nf.test @@ -2,8 +2,6 @@ nextflow_pipeline { name "Test pipeline with STAR aligner and RSEM for quantification" script "../main.nf" - tag "rnaseq" - tag "PIPELINE" test("Default profile test") { From 153a9a16ddabd13a904850dc7dd23e1392a6c470 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:32:14 +0100 Subject: [PATCH 3/7] CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 849133fbc..71326f359 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -93,7 +93,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1324](https://github.com/nf-core/rnaseq/pull/1324) - Fix tags entries and rename pipeline level tests - [PR #1325](https://github.com/nf-core/rnaseq/pull/1325) - Minor fixes to strandedness settings and messaging - [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file -- [PR #####]() - Add pipeline level test for STAR-RSEM and HISAT2 +- [PR #1328](https://github.com/nf-core/rnaseq/pull/1328) - Add pipeline level test for STAR-RSEM and HISAT2 ### Parameters From 7cda5c26d0c01bb6a10661cf673706c760ab9784 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:33:35 +0100 Subject: [PATCH 4/7] test naming conventions --- tests/hisat2.main.nf.test | 2 +- tests/star_rsem.main.nf.test | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/hisat2.main.nf.test b/tests/hisat2.main.nf.test index a20302422..69fdd5e33 100644 --- a/tests/hisat2.main.nf.test +++ b/tests/hisat2.main.nf.test @@ -3,7 +3,7 @@ nextflow_pipeline { name "Test pipeline with HISAT2 aligner" script "../main.nf" - test("Default profile test") { + test("Params: --aligner hisat2") { when { params { diff --git a/tests/star_rsem.main.nf.test b/tests/star_rsem.main.nf.test index 75e0f9f1b..07cfccbbc 100644 --- a/tests/star_rsem.main.nf.test +++ b/tests/star_rsem.main.nf.test @@ -3,7 +3,7 @@ nextflow_pipeline { name "Test pipeline with STAR aligner and RSEM for quantification" script "../main.nf" - test("Default profile test") { + test("Params: --aligner star_rsem") { when { params { From 43c709f5d0783852f4603041234fa18bf672073e Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:46:47 +0100 Subject: [PATCH 5/7] Update tests/hisat2.main.nf.test Co-authored-by: Harshil Patel --- tests/hisat2.main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/hisat2.main.nf.test b/tests/hisat2.main.nf.test index 69fdd5e33..c8b55906e 100644 --- a/tests/hisat2.main.nf.test +++ b/tests/hisat2.main.nf.test @@ -8,7 +8,7 @@ nextflow_pipeline { when { params { outdir = "$outputDir" - aligner = 'hisat2' + aligner = 'hisat2' } } From 3acbeb84f6f7bcdb0742ce05ea98f8a4ba74c530 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:46:52 +0100 Subject: [PATCH 6/7] Update tests/star_rsem.main.nf.test Co-authored-by: Harshil Patel --- tests/star_rsem.main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/star_rsem.main.nf.test b/tests/star_rsem.main.nf.test index 07cfccbbc..3a0b867a9 100644 --- a/tests/star_rsem.main.nf.test +++ b/tests/star_rsem.main.nf.test @@ -8,7 +8,7 @@ nextflow_pipeline { when { params { outdir = "$outputDir" - aligner = 'star_rsem' + aligner = 'star_rsem' } } From 0e5cc2cb23f1a60499fbf92a91eec44d2d0800a1 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:49:44 +0100 Subject: [PATCH 7/7] Rename files in line with other tests --- tests/{hisat2.main.nf.test => hisat2.nf.test} | 0 tests/{star_rsem.main.nf.test => star_rsem.nf.test} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename tests/{hisat2.main.nf.test => hisat2.nf.test} (100%) rename tests/{star_rsem.main.nf.test => star_rsem.nf.test} (100%) diff --git a/tests/hisat2.main.nf.test b/tests/hisat2.nf.test similarity index 100% rename from tests/hisat2.main.nf.test rename to tests/hisat2.nf.test diff --git a/tests/star_rsem.main.nf.test b/tests/star_rsem.nf.test similarity index 100% rename from tests/star_rsem.main.nf.test rename to tests/star_rsem.nf.test