Adding extra meta-fields for sentieon/bwamem (nf-core#3717)

Adding extra meta-fields for fasta and fai
JPejovicApis · Oct 10, 2023 · e726e24 · e726e24
1 parent 76e3ac5
commit e726e24
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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] )
 }