From 2bccce19bfc5880dd96cce5cc53cdb3fb8eb8070 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 10:24:55 +0200 Subject: [PATCH 1/4] fixed matrix.test_name in linting --- .github/workflows/ci.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b49a5fc..407121b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,6 +35,10 @@ jobs: - "singularity" test_name: - "test" + - "test_long" + - "test_long_miniasm" + - "test_hybrid" + - "test_dfast" isMaster: - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev From fd2b54e814f2d73961f8f288ae7c73159450a645 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 11:34:00 +0200 Subject: [PATCH 2/4] remove parameter section in git ci --- .github/workflows/ci.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 407121b..e234aaa 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -47,12 +47,6 @@ jobs: profile: "conda" - isMaster: false profile: "singularity" - parameters: - - "test" - - "test_long" - - "test_long_miniasm" - - "test_hybrid" - - "test_dfast" steps: - name: Check out pipeline code From 85bdf8540dc7fb2b1ae37cc353eaa5f3c500e068 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 11:57:56 +0200 Subject: [PATCH 3/4] implement missing features in memory set up from nf-core tools 3.0.2 --- assets/schema_input.json | 4 ---- conf/test_dfast.config | 14 +++++++++----- conf/test_full.config | 9 +++++++++ conf/test_hybrid.config | 14 +++++++++----- conf/test_hybrid_dragonflye.config | 14 +++++++++----- conf/test_long.config | 14 +++++++++----- conf/test_long_dragonflye.config | 8 ++++++++ conf/test_long_miniasm.config | 14 +++++++++----- 8 files changed, 62 insertions(+), 29 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 3cf372d..8758726 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -19,7 +19,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$" }, { @@ -33,7 +32,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$" }, { @@ -47,7 +45,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$" }, { @@ -61,7 +58,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\/[\\S\\s]*|NA)$" }, { diff --git a/conf/test_dfast.config b/conf/test_dfast.config index e2d0afe..ada68c6 100644 --- a/conf/test_dfast.config +++ b/conf/test_dfast.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test_dfast profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv' diff --git a/conf/test_full.config b/conf/test_full.config index f3dc621..6535fd4 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,15 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config index a524de0..3ddad51 100644 --- a/conf/test_hybrid.config +++ b/conf/test_hybrid.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid.tsv' diff --git a/conf/test_hybrid_dragonflye.config b/conf/test_hybrid_dragonflye.config index 9cf3436..349c540 100644 --- a/conf/test_hybrid_dragonflye.config +++ b/conf/test_hybrid_dragonflye.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test hybrid-dragonflye profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid_dragonflye.tsv' diff --git a/conf/test_long.config b/conf/test_long.config index 3cc3a8b..3ebc421 100644 --- a/conf/test_long.config +++ b/conf/test_long.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test_long profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv' diff --git a/conf/test_long_dragonflye.config b/conf/test_long_dragonflye.config index 38301d4..07f1bf5 100644 --- a/conf/test_long_dragonflye.config +++ b/conf/test_long_dragonflye.config @@ -9,6 +9,14 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test_long_dragonfyle profile' diff --git a/conf/test_long_miniasm.config b/conf/test_long_miniasm.config index d6b5874..ab2dd10 100644 --- a/conf/test_long_miniasm.config +++ b/conf/test_long_miniasm.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test_long_miniasm profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv' From aa42f9517977013b6340a34a44ecdd42b61a3580 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 11:59:43 +0200 Subject: [PATCH 4/4] update changelog #179 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 33ee3cd..8ea7ef2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#179](https://github.com/nf-core/bacass/pull/179) Fixed matrix.test_name in linting and missing features from template 3.0.2. - [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample. - [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel. - [#168](https://github.com/nf-core/bacass/pull/168) Fix wrong metadata in canu input channel.