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Code review for release 2.4.0 #184

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merged 2 commits into from
Nov 18, 2024
Merged

Code review for release 2.4.0 #184

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bf367e4
added code review from #181
Daniel-VM Nov 18, 2024
cd1bf3e
fix linting in #184
Daniel-VM Nov 18, 2024
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1 change: 1 addition & 0 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -20,6 +20,7 @@ jobs:
steps:
- uses: octokit/[email protected]
id: check_approvals
if: github.event_name != 'workflow_dispatch'
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
env:
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -18,5 +18,5 @@ template:
outdir: .
skip_features:
- igenomes
version: 2.4.0dev
version: 2.4.0
update: null
5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion conf/base.config
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Expand Up @@ -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
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3 changes: 0 additions & 3 deletions conf/modules.config
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Expand Up @@ -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'}
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maxRetries = 3

ext.args = ''
publishDir = [
path: { "${params.outdir}/Kmerfinder/${meta.id}" },
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3 changes: 0 additions & 3 deletions workflows/bacass.nf
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Expand Up @@ -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
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