diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index dd5acbf..3d60a62 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -20,6 +20,7 @@ jobs: steps: - uses: octokit/request-action@v2.x id: check_approvals + if: github.event_name != 'workflow_dispatch' with: route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews env: diff --git a/.nf-core.yml b/.nf-core.yml index 84c59be..875c078 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,5 +18,5 @@ template: outdir: . skip_features: - igenomes - version: 2.4.0dev + version: 2.4.0 update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index 950287d..7594ac2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -35,6 +35,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` +| Tool | Previous version | New version | +| --------- | ---------------- | ----------- | +| Dfast | 1.2.20 | 1.3.2 | +| Unicycler | 0.4.8 | 0.5.0 | + ### `Deprecated` ## v2.3.1 nf-core/bacass: "Navy Iron Oyster" 2024/06/24 diff --git a/conf/base.config b/conf/base.config index 5dc3f9e..bad115d 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } - maxRetries = 1 + maxRetries = 3 maxErrors = '-1' // Process-specific resource requirements diff --git a/conf/modules.config b/conf/modules.config index 0324168..7b0bc4a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -299,9 +299,6 @@ if (!params.skip_fastp) { if (!params.skip_kmerfinder) { process { withName: '.*:.*:KMERFINDER_SUBWORKFLOW:KMERFINDER' { - errorStrategy = { task.exitStatus in [1, 137, 139] ? 'retry' : 'finish'} - maxRetries = 3 - ext.args = '' publishDir = [ path: { "${params.outdir}/Kmerfinder/${meta.id}" }, diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 293056c..fed8253 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -60,9 +60,6 @@ include { methodsDescriptionText } from '../subworkflows/local/ut def checkPathParamList = [ params.input, params.multiqc_config, params.kraken2db, params.dfast_config ] for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } -// Place config files here - - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW