diff --git a/conf/base.config b/conf/base.config
index 6af79a7b..6af45542 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -14,12 +14,6 @@ process {
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
diff --git a/main.nf b/main.nf
index b5b499d5..b461a4e3 100644
--- a/main.nf
+++ b/main.nf
@@ -83,6 +83,46 @@ workflow {
     )
 }
 
+output {
+    path params.outdir
+
+    collect('fastq') {
+        select('ASPERA_CLI|SRA_FASTQ_FTP|SRATOOLS_FASTERQDUMP') {
+            path 'fastq'
+            pattern '*.fastq.gz'
+        }
+
+        select('ASPERA_CLI|SRA_FASTQ_FTP') {
+            path 'fastq/md5'
+            pattern '*.md5'
+        }
+    }
+
+    collect('metadata') {
+        path 'metadata'
+        select('SRA_RUNINFO_TO_FTP') {
+            pattern '*.tsv'
+        }
+    }
+
+    collect('samplesheet') {
+        path 'samplesheet'
+        select('MULTIQC_MAPPINGS_CONFIG') {
+            pattern 'multiqc_config.yml'
+        }
+
+        // index {
+        //     format 'csv'
+        //     path 'id_mappings.csv'
+        // }
+
+        // index {
+        //     format 'csv'
+        //     path 'samplesheet.csv'
+        // }
+    }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
diff --git a/modules/local/aspera_cli/nextflow.config b/modules/local/aspera_cli/nextflow.config
index fa2dbd90..9a808242 100644
--- a/modules/local/aspera_cli/nextflow.config
+++ b/modules/local/aspera_cli/nextflow.config
@@ -1,17 +1,5 @@
 process {
     withName: 'ASPERA_CLI' {
         ext.args = '-QT -l 300m -P33001'
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
-                mode: params.publish_dir_mode,
-                pattern: "*.md5"
-            ]
-        ]
     }
 }
diff --git a/modules/local/multiqc_mappings_config/nextflow.config b/modules/local/multiqc_mappings_config/nextflow.config
deleted file mode 100644
index 11c58341..00000000
--- a/modules/local/multiqc_mappings_config/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: 'MULTIQC_MAPPINGS_CONFIG' {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/modules/local/sra_fastq_ftp/nextflow.config b/modules/local/sra_fastq_ftp/nextflow.config
index 56e43959..26261f26 100644
--- a/modules/local/sra_fastq_ftp/nextflow.config
+++ b/modules/local/sra_fastq_ftp/nextflow.config
@@ -1,17 +1,5 @@
 process {
     withName: 'SRA_FASTQ_FTP' {
         ext.args = '-t 5 -nv -c -T 60'
-        publishDir = [
-            [
-                path: { "${params.outdir}/fastq" },
-                mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ],
-            [
-                path: { "${params.outdir}/fastq/md5" },
-                mode: params.publish_dir_mode,
-                pattern: "*.md5"
-            ]
-        ]
     }
 }
diff --git a/modules/local/sra_ids_to_runinfo/nextflow.config b/modules/local/sra_ids_to_runinfo/nextflow.config
deleted file mode 100644
index 9b9d0b16..00000000
--- a/modules/local/sra_ids_to_runinfo/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-    withName: 'SRA_IDS_TO_RUNINFO' {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            enabled: false
-        ]
-    }
-}
diff --git a/modules/local/sra_runinfo_to_ftp/nextflow.config b/modules/local/sra_runinfo_to_ftp/nextflow.config
deleted file mode 100644
index 43263648..00000000
--- a/modules/local/sra_runinfo_to_ftp/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: 'SRA_RUNINFO_TO_FTP' {
-        publishDir = [
-            path: { "${params.outdir}/metadata" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/modules/local/sra_to_samplesheet/nextflow.config b/modules/local/sra_to_samplesheet/nextflow.config
deleted file mode 100644
index da241c1a..00000000
--- a/modules/local/sra_to_samplesheet/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-    withName: SRA_TO_SAMPLESHEET {
-        publishDir = [
-            path: { "${params.outdir}/samplesheet" },
-            enabled: false
-        ]
-    }
-}
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
index c4a96e94..df5def04 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
@@ -4,8 +4,6 @@ params.settings_file = "${params.settings_path}/user-settings.mkfg"
 env.NCBI_SETTINGS = params.settings_file
 
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: CUSTOM_SRATOOLSNCBISETTINGS {
         containerOptions = {
             (workflow.containerEngine == 'singularity') ?
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
index f98b140d..7e1649d1 100644
--- a/modules/nf-core/sratools/fasterqdump/nextflow.config
+++ b/modules/nf-core/sratools/fasterqdump/nextflow.config
@@ -1,10 +1,5 @@
 process {
     withName: SRATOOLS_FASTERQDUMP {
         ext.args = '--split-files --include-technical'
-        publishDir = [
-            path: { "${params.outdir}/fastq" },
-            mode: params.publish_dir_mode,
-            pattern: "*.fastq.gz"
-        ]
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
deleted file mode 100644
index a2ca8848..00000000
--- a/modules/nf-core/sratools/prefetch/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-    withName: SRATOOLS_PREFETCH {
-        publishDir = [
-            path: { "${params.outdir}/sra" },
-            enabled: false
-        ]
-    }
-}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
index de803a38..187faf6d 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
@@ -1,2 +1 @@
-includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config'
 includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config'
diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
index d242c238..522b05b8 100644
--- a/workflows/sra/nextflow.config
+++ b/workflows/sra/nextflow.config
@@ -1,8 +1,3 @@
-includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config"
 includeConfig "../../modules/local/aspera_cli/nextflow.config"
 includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
-includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
-includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
-includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
-includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"
 includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config"