Add a flag to control FTP export

If true, it runs. Used to disable a full ftp export for the weekly pipeline
RNAcentral · Oct 10, 2023 · bf0ad06 · bf0ad06
1 parent d303d7e
commit bf0ad06
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Showing 2 changed files with 19 additions and 17 deletions.
diff --git a/config/export.config b/config/export.config
@@ -32,6 +32,7 @@ params {
     }
 
     ftp {
+      run= true
       publish = "${baseDir}/ftp"
       id_mapping {
         run = true
@@ -84,4 +85,3 @@ params {
     }
   }
 }
-
diff --git a/workflows/export/ftp.nf b/workflows/export/ftp.nf
@@ -98,22 +98,24 @@ process gpi {
 workflow ftp {
   take: _flag
   main:
-    Channel.fromPath('files/ftp-export/md5/md5.sql') | set { md5_query }
-    Channel.fromPath('files/ftp-export/md5/readme.txt') | set { md5_template }
-    md5(md5_query, md5_template)
-
-    Channel.fromPath('files/ftp-export/release_note.txt') | release_note
-    Channel.fromPath('files/ftp-export/go_annotations/rnacentral_rfam_annotations.sql') | rfam_go_matches
-
-    Channel.fromPath('files/ftp-export/rfam/rfam-annotations.sql') | set { rfam_annotation_query }
-    Channel.fromPath('files/ftp-export/rfam/readme.txt') | set { rfam_readme }
-    rfam_annotations(rfam_annotation_query, rfam_readme)
-
-    gpi()
-    id_mapping()
-    export_coordinates()
-    ensembl_export()
-    fasta_export()
+    if (params.export.ftp.run) {
+      Channel.fromPath('files/ftp-export/md5/md5.sql') | set { md5_query }
+      Channel.fromPath('files/ftp-export/md5/readme.txt') | set { md5_template }
+      md5(md5_query, md5_template)
+
+      Channel.fromPath('files/ftp-export/release_note.txt') | release_note
+      Channel.fromPath('files/ftp-export/go_annotations/rnacentral_rfam_annotations.sql') | rfam_go_matches
+
+      Channel.fromPath('files/ftp-export/rfam/rfam-annotations.sql') | set { rfam_annotation_query }
+      Channel.fromPath('files/ftp-export/rfam/readme.txt') | set { rfam_readme }
+      rfam_annotations(rfam_annotation_query, rfam_readme)
+
+      gpi()
+      id_mapping()
+      export_coordinates()
+      ensembl_export()
+      fasta_export()
+    }
 }
 
 workflow {