fixed execution of versions file generation

fmalmeida · Feb 24, 2024 · de97097 · de97097
1 parent a108dc2
commit de97097
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Showing 7 changed files with 36 additions and 39 deletions.
diff --git a/conf/docker.config b/conf/docker.config
@@ -4,8 +4,4 @@ singularity.enabled     = false
 docker.enabled          = true
 docker.runOptions       = '-u \$(id -u):\$(id -g)'
 fixOwnership            = true
-process {
-    withName: '.*' {
-        container = "fmalmeida/mpgap@sha256:6cd3680958574a8a6c427ea7f31172c44d50cdb960d71e85a6b44eae3c7afc80"
-    }
-}
+process.container       = "fmalmeida/mpgap@sha256:6cd3680958574a8a6c427ea7f31172c44d50cdb960d71e85a6b44eae3c7afc80"
diff --git a/conf/singularity.config b/conf/singularity.config
@@ -3,8 +3,4 @@ params.selected_profile = "singularity"
 docker.enabled          = false
 singularity.enabled     = true
 singularity.autoMounts  = true
-process {
-    withName: '.*' {
-        container = "docker://fmalmeida/mpgap@sha256:6cd3680958574a8a6c427ea7f31172c44d50cdb960d71e85a6b44eae3c7afc80"
-    }
-}
+process.container       = "docker://fmalmeida/mpgap@sha256:6cd3680958574a8a6c427ea7f31172c44d50cdb960d71e85a6b44eae3c7afc80"
diff --git a/nextflow.config b/nextflow.config
@@ -12,7 +12,12 @@ includeConfig 'conf/base.config'
 params.hybrid_strategy = params.hybrid_strategy.toString()
 
 // not save version by default
-process { publishDir = [ saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] }
+process {
+  publishDir = [ 
+    path: params.output,
+    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+  ]
+}
 
 
 // Nextflow management

diff --git a/workflows/assembly_qc.nf b/workflows/assembly_qc.nf
diff --git a/workflows/hybrid.nf b/workflows/hybrid.nf
diff --git a/workflows/long-reads-only.nf b/workflows/long-reads-only.nf
diff --git a/workflows/short-reads-only.nf b/workflows/short-reads-only.nf