From 691feeafdcd8b7874f540695ece122cce01a524f Mon Sep 17 00:00:00 2001
From: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
Date: Tue, 16 Nov 2021 15:09:30 +0100
Subject: [PATCH] GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split
 into separate input channels (#1076)

* fasta_fai_dict tuple is now split into separate input channels

* fix: lint errors

* fix: pytest errors

* Update modules/gatk4/splitncigarreads/meta.yml

* Update modules/gatk4/splitncigarreads/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 modules/gatk4/splitncigarreads/main.nf       |  4 +++-
 modules/gatk4/splitncigarreads/meta.yml      | 15 +++++++++++----
 tests/modules/gatk4/splitncigarreads/main.nf |  9 ++++-----
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index 01b1d05a..26fb799d 100644
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@@ -20,7 +20,9 @@ process GATK4_SPLITNCIGARREADS {
 
     input:
     tuple val(meta), path(bam)
-    tuple path(fasta), path(fai), path(dict)
+    path  fasta
+    path  fai
+    path  dict
 
     output:
     tuple val(meta), path('*.bam'), emit: bam
diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml
index f287ede4..fd6edda0 100644
--- a/modules/gatk4/splitncigarreads/meta.yml
+++ b/modules/gatk4/splitncigarreads/meta.yml
@@ -24,10 +24,17 @@ input:
       description: BAM/SAM/CRAM file containing reads
       pattern: "*.{bam,sam,cram}"
   - fasta:
-      type: tuple of files
-      description: |
-        Tuple of fasta file (first), sequence dict (second) and fasta index (third)
-      pattern: ["*.fasta", "*.dict", "*.fai"]
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "*.fasta.fai"
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
 output:
   - bam:
       type: file
diff --git a/tests/modules/gatk4/splitncigarreads/main.nf b/tests/modules/gatk4/splitncigarreads/main.nf
index 3e6bde80..0934593f 100644
--- a/tests/modules/gatk4/splitncigarreads/main.nf
+++ b/tests/modules/gatk4/splitncigarreads/main.nf
@@ -8,10 +8,9 @@ workflow test_gatk4_splitncigarreads {
     input = [ [ id:'test' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] 
             ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
 
-    GATK4_SPLITNCIGARREADS ( input, fasta )
+    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
 }