From c39373703d8a8495f5ffab327556f17867e8d8a0 Mon Sep 17 00:00:00 2001 From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Date: Tue, 1 Oct 2024 14:59:08 +0100 Subject: [PATCH 1/9] Update README.md Adding DOI --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b8e17ab..5c42432 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ [![GitHub Actions CI Status](https://github.com/sanger-tol/ear/actions/workflows/ci.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/sanger-tol/ear/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions Linting Status](https://github.com/sanger-tol/ear/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/ear/actions/workflows/linting.yml)[![DOI](https://zenodo.org/badge/833605808.svg)](https://doi.org/10.5281/zenodo.13819520) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) From e7e4fc3e6873d69278c682b10d46347aba53e383 Mon Sep 17 00:00:00 2001 From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Date: Tue, 1 Oct 2024 15:00:23 +0100 Subject: [PATCH 2/9] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 83055b9..6e8499e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -225,7 +225,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=24.04.0' version = '0.6.0' - doi = '' + doi = 'https://zenodo.org/records/13819520' } // Load modules.config for DSL2 module specific options From 79a12a03ec0998299575ac4b5ce935bbc955703d Mon Sep 17 00:00:00 2001 From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:42:18 +0100 Subject: [PATCH 3/9] Update modules.config Moving btk to tagged version 0.6.0 --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 73e83bb..90a7a0e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -42,7 +42,7 @@ process { ext.executor = "bsub -Is -tty -e test.e -o test.log -n 2 -q oversubscribed -M1400 -R'select[mem>1400] rusage[mem=1400] span[hosts=1]'" ext.profiles = "singularity,sanger" ext.get_versions = "lsid | head -n1 | cut -d ',' -f 1" - ext.version = "draft_assemblies" + ext.version = "0.6.0" } withName: SANGER_TOL_CPRETEXT { From 2fbf4124573a7dfb3329af5ff15c3c90b1ef5755 Mon Sep 17 00:00:00 2001 From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:44:39 +0100 Subject: [PATCH 4/9] Update CHANGELOG.md Update --- CHANGELOG.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ebb5ba..d921035 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). Naming based on: [Mythical creatures](https://en.wikipedia.org/wiki/List_of_legendary_creatures_by_type). +## v1.0.1 - Robert Beiny H1 [08/10/2024] +- Blobtookit version was specified in the wrong location, so defaulted to a development branch "draft_assemblies", this has now been updated to v0.6.0. +- Zenodo DOI has now been added to the repo. + ## v1.0.0 - Robert Beiny [20/09/2024] Initial release of sanger-tol/ear, created with the [nf-core](https://nf-co.re/) template. @@ -36,8 +40,6 @@ CURATIONPRETEXT to generate pretext plots and pngs. | SAMTOOLS_MERGE | | 1.20--h50ea8bc_0 | | SAMTOOLS_SORT | | 1.20--h50ea8bc_0 | -| - \* for pipelines, please check their own CHANGELOG file for a full list of software dependencies. ### Dependencies From a126d8a0708db088e17a460e53c63448a3cc526b Mon Sep 17 00:00:00 2001 From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:46:01 +0100 Subject: [PATCH 5/9] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 6e8499e..c278c76 100644 --- a/nextflow.config +++ b/nextflow.config @@ -224,7 +224,7 @@ manifest { description = """ERGA Assembly Report pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.0' - version = '0.6.0' + version = '0.6.1' doi = 'https://zenodo.org/records/13819520' } From 2d2ac6bec02cda6d711bee1628280b15bfe6e7eb Mon Sep 17 00:00:00 2001 From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:46:25 +0100 Subject: [PATCH 6/9] Update CHANGELOG.md Correct version information --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d921035..2bb9758 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,11 +4,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). Naming based on: [Mythical creatures](https://en.wikipedia.org/wiki/List_of_legendary_creatures_by_type). -## v1.0.1 - Robert Beiny H1 [08/10/2024] +## v0.6.1 - Robert Beiny H1 [08/10/2024] - Blobtookit version was specified in the wrong location, so defaulted to a development branch "draft_assemblies", this has now been updated to v0.6.0. - Zenodo DOI has now been added to the repo. -## v1.0.0 - Robert Beiny [20/09/2024] +## v0.6.0 - Robert Beiny [20/09/2024] Initial release of sanger-tol/ear, created with the [nf-core](https://nf-co.re/) template. The current pipeline means the MVP for ear. From dfb79a09ca41119c2befbfd5a719779cde65b1c1 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 8 Oct 2024 08:54:07 +0100 Subject: [PATCH 7/9] updating version info and fixing linting error --- conf/base.config | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index aa5a770..f600868 100644 --- a/conf/base.config +++ b/conf/base.config @@ -23,7 +23,7 @@ process { time = { check_max( 70.h * task.attempt, 'time' ) } } - withName: "MINIMAP2_ALIGN_SE" { + withName: "MINIMAP2_ALIGN_SE" { cpus = { check_max( 16 , 'cpus' ) } memory = { check_max( 1.GB * ( reference.size() < 2e9 ? 40 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * task.attempt ) , 'memory') } time = { check_max( 1.h * ( reference.size() < 1e9 ? 10 : reference.size() < 10e9 ? 30 : 48), 'time' ) } @@ -36,35 +36,43 @@ process { // adding in your local modules too. // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors + withLabel:process_single { cpus = { check_max( 1 , 'cpus' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } } + withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } } + withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } memory = { check_max( 36.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } + withLabel:process_high { cpus = { check_max( 12 * task.attempt, 'cpus' ) } memory = { check_max( 72.GB * task.attempt, 'memory' ) } time = { check_max( 16.h * task.attempt, 'time' ) } } + withLabel:process_long { time = { check_max( 20.h * task.attempt, 'time' ) } } + withLabel:process_high_memory { memory = { check_max( 200.GB * task.attempt, 'memory' ) } } + withLabel:error_ignore { errorStrategy = 'ignore' } + withLabel:error_retry { errorStrategy = 'retry' maxRetries = 2 From 01baf9287701c33ddf0e025efc068a19b9e0f6b3 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 8 Oct 2024 08:54:58 +0100 Subject: [PATCH 8/9] Prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2bb9758..ff4ec69 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 Naming based on: [Mythical creatures](https://en.wikipedia.org/wiki/List_of_legendary_creatures_by_type). ## v0.6.1 - Robert Beiny H1 [08/10/2024] + - Blobtookit version was specified in the wrong location, so defaulted to a development branch "draft_assemblies", this has now been updated to v0.6.0. - Zenodo DOI has now been added to the repo. From 8127c7c2c811e2084d94737e801d6145748b3544 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 8 Oct 2024 08:56:18 +0100 Subject: [PATCH 9/9] New line for editorconfig --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index 138ff19..ac4a5f3 100644 --- a/LICENSE +++ b/LICENSE @@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. \ No newline at end of file +SOFTWARE.