Merge pull request #10 from sanger-tol/DLBPointon-patch-1

Dlb pointon patch 1
sanger-tol · Oct 8, 2024 · 20cb5a4 · 20cb5a4
2 parents 828cf7c + 8127c7c
commit 20cb5a4
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diff --git 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
@@ -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.
+SOFTWARE.
diff --git 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
@@ -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
@@ -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
@@ -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