diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ebb5ba..ff4ec69 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,12 @@ 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). -## v1.0.0 - Robert Beiny [20/09/2024] +## 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. + +## 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. @@ -36,8 +41,6 @@ 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 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. 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/) 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 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 { diff --git a/nextflow.config b/nextflow.config index 83055b9..c278c76 100644 --- a/nextflow.config +++ b/nextflow.config @@ -224,8 +224,8 @@ manifest { description = """ERGA Assembly Report pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.0' - version = '0.6.0' - doi = '' + version = '0.6.1' + doi = 'https://zenodo.org/records/13819520' } // Load modules.config for DSL2 module specific options