Add output definition

Signed-off-by: Ben Sherman <[email protected]>
nf-core · Feb 28, 2024 · b8dd9e2 · b8dd9e2
1 parent b03ed3b
commit b8dd9e2
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Showing 13 changed files with 40 additions and 85 deletions.
diff --git 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
@@ -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
@@ -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
diff --git 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
diff --git a/modules/local/sra_runinfo_to_ftp/nextflow.config b/modules/local/sra_runinfo_to_ftp/nextflow.config
diff --git a/modules/local/sra_to_samplesheet/nextflow.config b/modules/local/sra_to_samplesheet/nextflow.config
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config
diff --git 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"