From adf071fbc2235ee4ef5789aa77410c976d1e94e8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20B=C3=A4uerle?=
 <45968370+famosab@users.noreply.github.com>
Date: Wed, 30 Oct 2024 11:26:14 +0100
Subject: [PATCH] adjust io of fq2bam to be consistent (#6906)

* adjust io to be consistent

* adjust meta to be consistent

* fix meta
---
 modules/nf-core/parabricks/fq2bam/main.nf     |  4 ++--
 modules/nf-core/parabricks/fq2bam/meta.yml    | 23 +++++++++++++------
 .../parabricks/fq2bam/tests/main.nf.test      |  8 +++----
 3 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/parabricks/fq2bam/main.nf b/modules/nf-core/parabricks/fq2bam/main.nf
index a68a64bf948..c1877bdf468 100644
--- a/modules/nf-core/parabricks/fq2bam/main.nf
+++ b/modules/nf-core/parabricks/fq2bam/main.nf
@@ -8,15 +8,15 @@ process PARABRICKS_FQ2BAM {
     tuple val(meta), path(reads)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(index)
-    path(interval_file)
+    tuple val(meta4), path(interval_file)
     path(known_sites)
 
     output:
     tuple val(meta), path("*.bam")  , emit: bam
     tuple val(meta), path("*.bai")  , emit: bai
+    tuple val(meta), path("*.table"), emit: bqsr_table          , optional:true
     path "versions.yml"             , emit: versions
     path "qc_metrics"               , emit: qc_metrics          , optional:true
-    path("*.table")                 , emit: bqsr_table          , optional:true
     path("duplicate-metrics.txt")   , emit: duplicate_metrics   , optional:true
 
     when:
diff --git a/modules/nf-core/parabricks/fq2bam/meta.yml b/modules/nf-core/parabricks/fq2bam/meta.yml
index b1cae9c4fa4..b3e2e7e6ee6 100644
--- a/modules/nf-core/parabricks/fq2bam/meta.yml
+++ b/modules/nf-core/parabricks/fq2bam/meta.yml
@@ -40,7 +40,11 @@ input:
         type: file
         description: reference BWA index
         pattern: "*.{amb,ann,bwt,pac,sa}"
-  - - interval_file:
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing index information
+    - interval_file:
         type: file
         description: (optional) file(s) containing genomic intervals for use in base
           quality score recalibration (BQSR)
@@ -71,6 +75,17 @@ output:
           type: file
           description: index corresponding to sorted BAM file
           pattern: "*.bai"
+  - bqsr_table:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test']
+      - "*.table":
+          type: file
+          description: (optional) table from base quality score recalibration calculation,
+            to be used with parabricks/applybqsr
+          pattern: "*.table"
   - versions:
       - versions.yml:
           type: file
@@ -81,12 +96,6 @@ output:
           type: directory
           description: (optional) optional directory of qc metrics
           pattern: "qc_metrics"
-  - bqsr_table:
-      - "*.table":
-          type: file
-          description: (optional) table from base quality score recalibration calculation,
-            to be used with parabricks/applybqsr
-          pattern: "*.table"
   - duplicate_metrics:
       - duplicate-metrics.txt:
           type: file
diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
index 46d06322c32..8e4adb2966c 100644
--- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
+++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
@@ -53,7 +53,7 @@ nextflow_process {
                     file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWA_INDEX.out.index
-                input[3] = []
+                input[3] = [ [], [] ]
                 input[4] = []
                 """
             }
@@ -88,7 +88,7 @@ nextflow_process {
                     file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
                 ])
 				input[2] = BWA_INDEX.out.index
-                input[3] = []
+                input[3] = [ [], [] ]
                 input[4] = []
                 """
             }
@@ -119,7 +119,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = BWA_INDEX_PE.out.index
-                input[3] = []
+                input[3] = [ [], [] ]
                 input[4] = []
                 """
             }
@@ -156,7 +156,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ])
                 input[2] = BWA_INDEX_PE.out.index
-                input[3] = []
+                input[3] = [ [], [] ]
                 input[4] = []
                 """
             }