diff --git a/CHANGELOG.md b/CHANGELOG.md
index 51c72ff5..72b253e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v1.2.1 - Bouncy Basenji Patch [2024-11-27]
+## v1.2.1 - Bouncy Basenji Patch [2024-11-28]
 
 ### `Added`
 
diff --git a/conf/test.config b/conf/test.config
index 51d28553..610a1d01 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -55,16 +55,40 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: MEGAN_RMA2INFO_TSV {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = "-c2c Taxonomy"
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{txt.gz,megan}'
+        ]
     }
     withName: MEGAN_RMA2INFO_KRONA {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "--read2class Taxonomy" }
+        ext.prefix = { "${meta.id}_${meta.db_name}" }
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_alternativepreprocessing.config b/conf/test_alternativepreprocessing.config
index 813a9f83..b67c06e2 100644
--- a/conf/test_alternativepreprocessing.config
+++ b/conf/test_alternativepreprocessing.config
@@ -51,10 +51,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_bbduk.config b/conf/test_bbduk.config
index 4de2e195..3dafb0ff 100644
--- a/conf/test_bbduk.config
+++ b/conf/test_bbduk.config
@@ -49,10 +49,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_falco.config b/conf/test_falco.config
index 43f93aed..17e11f37 100644
--- a/conf/test_falco.config
+++ b/conf/test_falco.config
@@ -49,10 +49,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_fastp.config b/conf/test_fastp.config
index 84e0782b..b59af972 100644
--- a/conf/test_fastp.config
+++ b/conf/test_fastp.config
@@ -51,10 +51,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_krakenuniq.config b/conf/test_krakenuniq.config
index 9f1862b4..3fb2791d 100644
--- a/conf/test_krakenuniq.config
+++ b/conf/test_krakenuniq.config
@@ -61,15 +61,40 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: MEGAN_RMA2INFO_TSV {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = "-c2c Taxonomy"
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{txt.gz,megan}'
+        ]
     }
     withName: MEGAN_RMA2INFO_KRONA {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "--read2class Taxonomy" }
+        ext.prefix = { "${meta.id}_${meta.db_name}" }
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_malt.config b/conf/test_malt.config
index 4bb5b44b..9e144d3d 100644
--- a/conf/test_malt.config
+++ b/conf/test_malt.config
@@ -53,9 +53,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_motus.config b/conf/test_motus.config
index f51e735c..fe9d3e0a 100644
--- a/conf/test_motus.config
+++ b/conf/test_motus.config
@@ -57,9 +57,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.config
index 537676e3..c31281d8 100644
--- a/conf/test_nopreprocessing.config
+++ b/conf/test_nopreprocessing.config
@@ -51,10 +51,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.config
index 39d52115..ea91f489 100644
--- a/conf/test_noprofiling.config
+++ b/conf/test_noprofiling.config
@@ -50,9 +50,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_nothing.config b/conf/test_nothing.config
index 5160093b..5d22558a 100644
--- a/conf/test_nothing.config
+++ b/conf/test_nothing.config
@@ -49,10 +49,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_prinseqplusplus.config b/conf/test_prinseqplusplus.config
index 9f4f4417..6abb95fa 100644
--- a/conf/test_prinseqplusplus.config
+++ b/conf/test_prinseqplusplus.config
@@ -50,10 +50,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/nextflow.config b/nextflow.config
index 77739126..f37fa63f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -193,6 +193,8 @@ params {
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
 
 profiles {
     debug {
@@ -414,6 +416,3 @@ validation {
         afterText = validation.help.afterText
     }
 }
-
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'