From c17d1a7a7b473e103ddd3f28bd91b79733aa7cf2 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 13:04:41 +0200
Subject: [PATCH] fix output glob (#1552)

---
 modules/elprep/filter/main.nf        | 4 ++--
 tests/modules/elprep/filter/test.yml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/elprep/filter/main.nf b/modules/elprep/filter/main.nf
index 02c93186..5ca288bc 100644
--- a/modules/elprep/filter/main.nf
+++ b/modules/elprep/filter/main.nf
@@ -23,7 +23,7 @@ process ELPREP_FILTER {
 
 
     output:
-    tuple val(meta), path("**.{bam,sam}")           ,emit: bam
+    tuple val(meta), path("output/**.{bam,sam}")    ,emit: bam
     tuple val(meta), path("*.metrics.txt")          ,optional: true, emit: metrics
     tuple val(meta), path("*.recall")               ,optional: true, emit: recall
     tuple val(meta), path("*.vcf.gz")               ,optional: true, emit: gvcf
@@ -65,7 +65,7 @@ process ELPREP_FILTER {
     def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
 
     """
-    elprep filter ${bam} ${prefix}.${suffix} \\
+    elprep filter ${bam} output/${prefix}.${suffix} \\
         ${reference_sequences_cmd} \\
         ${filter_regions_cmd} \\
         ${markdup_cmd} \\
diff --git a/tests/modules/elprep/filter/test.yml b/tests/modules/elprep/filter/test.yml
index 5242045b..922d7a9b 100644
--- a/tests/modules/elprep/filter/test.yml
+++ b/tests/modules/elprep/filter/test.yml
@@ -6,7 +6,7 @@
   files:
     - path: output/elprep/test.activity_profile.igv
     - path: output/elprep/test.assembly_regions.igv
-    - path: output/elprep/test.bam
+    - path: output/elprep/output/test.bam
     - path: output/elprep/test.g.vcf.gz
     - path: output/elprep/test.metrics.txt
     - path: output/elprep/test.recall