From 1487d5cf965840926d31e0034ec7c6ae990b33c0 Mon Sep 17 00:00:00 2001
From: Abhinav Sharma <abhi18av@users.noreply.github.com>
Date: Fri, 7 Aug 2020 11:07:31 +0530
Subject: [PATCH] fix the collate process

---
 main.nf | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 3a649a4..90d8a9a 100644
--- a/main.nf
+++ b/main.nf
@@ -60,9 +60,11 @@ Channel.fromPath("""${params.resultsDir}/results""")
         .set { ch_in_tbProfiler_collate }
 
 process tbProfiler_collate {
-    publishDir params.resultsDir, mode: params.saveMode
+    publishDir './', mode: params.saveMode
     container 'quay.io/biocontainers/tb-profiler:2.8.6--pypy_0'
 
+    echo true
+
     when:
     params.collate
 
@@ -70,20 +72,22 @@ process tbProfiler_collate {
     path("""${params.resultsDir}/results""") from ch_in_tbProfiler_collate
 
     output:
-    tuple path("""tbprofiler.dr.indiv.itol.txt"""),
-            path("""tbprofiler.dr.itol.txt"""),
-            path("""tbprofiler.json"""),
-            path("""tbprofiler.lineage.itol.txt"""),
-            path("""tbprofiler.txt"""),
-            path("""tbprofiler.variants.txt""") into ch_out_tbProfiler_collate
+    tuple file("""${params.resultsDir}/tbprofiler.dr.indiv.itol.txt"""),
+            file("""${params.resultsDir}/tbprofiler.dr.itol.txt"""),
+            file("""${params.resultsDir}/tbprofiler.json"""),
+            file("""${params.resultsDir}/tbprofiler.lineage.itol.txt"""),
+            file("""${params.resultsDir}/tbprofiler.txt"""),
+            file("""${params.resultsDir}/tbprofiler.variants.txt""") into ch_out_tbProfiler_collate
 
 
     script:
 
     """
+    cd $params.resultsDir
     tb-profiler update_tbdb
     tb-profiler collate
     """
+
 }