Merge pull request #184 from Daniel-VM/dev

Code review for release 2.4.0

.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:

.nf-core.yml

@@ -18,5 +18,5 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 2.4.0dev
+  version: 2.4.0
 update: null

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

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

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}" },

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