Fix publish dir [Close #20]

CLIMB-COVID · Mar 8, 2022 · 3e07d6b · 3e07d6b
1 parent 6e3f7b2
commit 3e07d6b
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diff --git a/modules/elan.nf b/modules/elan.nf
@@ -23,6 +23,7 @@ process resolve_uploads {
     output:
     path 'files.ls', emit: elan_files_manifest
     path 'files.err', emit: elan_files_unmatched
+    path manifest
 
     publishDir path: "${params.artifacts_root}/elan/${params.datestamp}/", pattern: "files.ls", mode: "copy", overwrite: true, saveAs: { filename -> "elan.manifest.ls" }
     publishDir path: "${params.artifacts_root}/elan/${params.datestamp}/", pattern: "files.err", mode: "copy", overwrite: true, saveAs: { filename -> "elan.missing.ls" }

diff --git a/workflows/elan.nf b/workflows/elan.nf
@@ -11,7 +11,7 @@ workflow inbound {
             saved_manifest = Channel.fromPath(params.inbound_manifest)
         }
         resolve_uploads(saved_manifest)
-        announce_uploads(saved_manifest, resolve_uploads.out)
+        announce_uploads(saved_manifest, resolve_uploads.out.elan_files_manifest, resolve_uploads.out.elan_files_unmatched)
 
         resolve_uploads.out.elan_files_manifest
             .splitCsv(header:[