Merge pull request #4 from nextflow-hub/develop

fix the collate process
nf-modules-hub · Aug 7, 2020 · 2e4eeb5 · 2e4eeb5
2 parents 5edf880 + 1487d5c
commit 2e4eeb5
Showing 1 changed file with 11 additions and 7 deletions.
diff --git a/main.nf b/main.nf
@@ -60,30 +60,34 @@ 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
 
     input:
     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
     """
+
 }