From db5a4298680697c92b6685eb77c426b2b7f68fbc Mon Sep 17 00:00:00 2001 From: pharmlovex Date: Tue, 29 Oct 2024 13:39:32 +0000 Subject: [PATCH 1/5] Fix: Missing import statements on error messages(#1566) --- subworkflows/local/utils_nfcore_sarek_pipeline/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf index a897dfebe5..f4983278a1 100644 --- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf @@ -349,7 +349,7 @@ def retrieveInput(need_input, step, outdir) { def input = null if (!params.input && !params.build_only_index) { switch (step) { - case 'mapping': Nextflow.error("Can't start with step $step without samplesheet") + case 'mapping': error("Can't start $step step without samplesheet") break case 'markduplicates': log.warn("Using file ${outdir}/csv/mapped.csv"); input = outdir + "/csv/mapped.csv" @@ -368,7 +368,7 @@ def retrieveInput(need_input, step, outdir) { input = outdir + "/csv/variantcalled.csv" break default: log.warn("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - Nextflow.error("Unknown step $step") + error("Unknown step $step") } } return input From 059b9ed553f9e7a866fde66757ddfb2097d7bbf8 Mon Sep 17 00:00:00 2001 From: pharmlovex Date: Tue, 29 Oct 2024 14:05:06 +0000 Subject: [PATCH 2/5] Update changelog for bug fixes --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a583aaf26..4130fdbf17 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test ### Fixed - +- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests - [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge From 823e87bb24444222603391276797c1563e77fb86 Mon Sep 17 00:00:00 2001 From: pharmlovex Date: Tue, 29 Oct 2024 16:25:00 +0000 Subject: [PATCH 3/5] Prettier formatted files --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4130fdbf17..603314ef56 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test ### Fixed + - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests From e6a6db84e991a41751550405af00df1a1e5715dd Mon Sep 17 00:00:00 2001 From: pharmlovex Date: Wed, 30 Oct 2024 07:48:09 +0000 Subject: [PATCH 4/5] modified changelog to follow sequence --- CHANGELOG.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 603314ef56..c27f2fccb5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed -- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests - [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge @@ -38,7 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1694](https://github.com/nf-core/sarek/pull/1694) - Fix manifest DOI display on CLI - [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json - [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode - +- [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet ### Removed - [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome` From 4087d6327badf793fa3f2e914b0e681bf59b66c9 Mon Sep 17 00:00:00 2001 From: pharmlovex Date: Wed, 30 Oct 2024 08:45:56 +0000 Subject: [PATCH 5/5] Formatting with prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c27f2fccb5..e14914386d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json - [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet + ### Removed - [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`