From 149b4746c6e16ef84f64db5bb245d5b9495fdc3f Mon Sep 17 00:00:00 2001
From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
Date: Thu, 10 Aug 2023 14:00:46 +0200
Subject: [PATCH] Adding extra meta-fields for sentieon/bwamem (#3717)

Adding extra meta-fields for fasta and fai
---
 modules/nf-core/sentieon/bwamem/main.nf       |  4 ++--
 modules/nf-core/sentieon/bwamem/meta.yml      | 10 ++++++++++
 tests/modules/nf-core/sentieon/bwamem/main.nf |  5 ++---
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
index aeca2825609..b58835fda54 100644
--- a/modules/nf-core/sentieon/bwamem/main.nf
+++ b/modules/nf-core/sentieon/bwamem/main.nf
@@ -10,8 +10,8 @@ process SENTIEON_BWAMEM {
     input:
     tuple val(meta), path(reads)
     tuple val(meta2), path(index)
-    path(fasta)
-    path(fasta_fai)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(fasta_fai)
 
     output:
     tuple val(meta), path("*.bam"), path("*.bai"), emit: bam_and_bai
diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml
index 3d1546c55dd..9987e8c9002 100644
--- a/modules/nf-core/sentieon/bwamem/meta.yml
+++ b/modules/nf-core/sentieon/bwamem/meta.yml
@@ -33,10 +33,20 @@ input:
       type: file
       description: BWA genome index files
       pattern: "*.{amb,ann,bwt,pac,sa}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Genome fasta file
       pattern: "*.{fa,fasta}"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
   - fasta_fai:
       type: file
       description: The index of the FASTA reference.
diff --git a/tests/modules/nf-core/sentieon/bwamem/main.nf b/tests/modules/nf-core/sentieon/bwamem/main.nf
index ab230e7f6ad..9b98915dff8 100644
--- a/tests/modules/nf-core/sentieon/bwamem/main.nf
+++ b/tests/modules/nf-core/sentieon/bwamem/main.nf
@@ -25,7 +25,7 @@ workflow test_sentieon_bwamem_single_end {
     ]
 
     SENTIEON_BWAINDEX ( fasta_ch )
-    SENTIEON_BWAMEM ( input_ch, SENTIEON_BWAINDEX.out.index, fasta_file, fasta_fai_file )
+    SENTIEON_BWAMEM ( input_ch, SENTIEON_BWAINDEX.out.index, fasta_ch, [[:], fasta_fai_file] )
 }
 
 
@@ -51,6 +51,5 @@ workflow test_sentieon_bwa_mem_paired_end {
     ]
 
     SENTIEON_BWAINDEX ( fasta_ch )
-    SENTIEON_BWAMEM ( input_ch, SENTIEON_BWAINDEX.out.index, fasta_file, fasta_fai_file )
-
+    SENTIEON_BWAMEM ( input_ch, SENTIEON_BWAINDEX.out.index, fasta_ch, [[:], fasta_fai_file] )
 }