Revert "Include CSVTK_JOIN"

This reverts commit b5bee2d.

Author: antoniasaracco

conf/modules.config

@@ -231,6 +231,11 @@ process {
     withName: DESEQ2_DIFFERENTIAL {
         ext.prefix = { "${meta.id}" }
         publishDir = [
+            [
+                path: { "${params.outdir}/tables/differential" },
+                mode: params.publish_dir_mode,
+                pattern: '*.deseq2.results.tsv'
+            ],
             [
                 path: { "${params.outdir}/plots/qc" },
                 mode: params.publish_dir_mode,
@@ -304,6 +309,11 @@ process {
     withName: LIMMA_DIFFERENTIAL {
         ext.prefix = { "${meta.id}" }
         publishDir = [
+            [
+                path: { "${params.outdir}/tables/differential" },
+                mode: params.publish_dir_mode,
+                pattern: '*.limma.results.tsv'
+            ],
             [
                 path: { "${params.outdir}/plots/qc" },
                 mode: params.publish_dir_mode,
@@ -338,38 +348,41 @@ process {
         ].join(' ').trim() }
     }
 
+    withName: VARIANCEPARTITION_DREAM {
+        publishDir = [
+            [
+                path: { "${params.outdir}/tables/differential" },
+                mode: params.publish_dir_mode,
+                pattern: '*.dream.results.tsv'
+            ]
+        ]
+    }
+
     withName: CUSTOM_FILTERDIFFERENTIALTABLE {
         ext.prefix = { "${input_file.toString().split("\\.").init().join(".")}" }
         publishDir = [
             [
-                path: { "${params.outdir}/tables/differential_filtered" },
+                path: { "${params.outdir}/tables/differential" },
                 mode: params.publish_dir_mode,
                 pattern: '*_filtered.tsv'
             ]
         ]
     }
 
     withName: CSVTK_JOIN {
-        ext.prefix = {
-            def method = meta.params.differential_method
-            def prefix = "${meta.id}_${method}.annotated"
-            return prefix
-        }
-        ext.args = { [
-            "--fields ${meta.params.features_id_col}",
-            "--left-join",
-            "-t",
-            "-k",
-            "-T",
-            "-D \$'\t'"
-        ].join(' ').trim() }
+        ext.prefix = { "${meta.id}.annotated" }
         publishDir = [
             [
                 path: { "${params.outdir}/tables/differential_annotated" },
                 mode: params.publish_dir_mode,
                 pattern: '*.tsv'
             ]
         ]
+        ext.args = { [
+            "--fields ${meta.params.features_id_col}",
+            "--left-join",
+            "-t"
+        ].join(' ').trim() }
     }
     // ==================================================================================
     // functional enrichment modules