Add haplotigs as possible input (#2834)

Co-authored-by: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
nf-core · Feb 7, 2023 · 7f59e57 · 7f59e57
1 parent c9968ab
commit 7f59e57
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Showing 3 changed files with 17 additions and 2 deletions.
diff --git a/modules/nf-core/merquryfk/merquryfk/main.nf b/modules/nf-core/merquryfk/merquryfk/main.nf
@@ -11,7 +11,7 @@ process MERQURYFK_MERQURYFK {
     }
 
     input:
-    tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly)
+    tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly), path(haplotigs)
 
     output:
     tuple val(meta), path("${prefix}.completeness.stats") , emit: stats
@@ -46,6 +46,7 @@ process MERQURYFK_MERQURYFK {
         -T$task.cpus \\
         ${fastk_ktab.find{ it.toString().endsWith(".ktab") }} \\
         $assembly \\
+        $haplotigs \\
         $prefix
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml
@@ -27,7 +27,11 @@ input:
       pattern: "*.ktab*"
   - assembly:
       type: file
-      description: Genome assembly files (fasta format)
+      description: Genome (primary) assembly files (fasta format)
+      pattern: ".fasta"
+  - haplotigs:
+      type: file
+      description: Assembly haplotigs (fasta format)
       pattern: ".fasta"
 
 output:

diff --git a/tests/modules/nf-core/merquryfk/merquryfk/main.nf b/tests/modules/nf-core/merquryfk/merquryfk/main.nf
@@ -16,10 +16,15 @@ workflow test_merquryfk_merquryfk_png {
         file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
+    haplotigs = [
+        [ id:'test', single_end:true ], []
+    ]
+
     FASTK_FASTK ( input )
     MERQURYFK_MERQURYFK ( FASTK_FASTK.out.hist
         .join( FASTK_FASTK.out.ktab )
         .join( Channel.value( assembly ) )
+        .join( Channel.value( haplotigs ) )
     )
 }
 
@@ -34,9 +39,14 @@ workflow test_merquryfk_merquryfk_pdf {
         file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
+    haplotigs = [
+        [ id:'test', single_end:true ], []
+    ]
+
     FASTK_FASTK ( input )
     MERQURYFK_MERQURYFK ( FASTK_FASTK.out.hist
         .join( FASTK_FASTK.out.ktab )
         .join( Channel.value( assembly ) )
+        .join( Channel.value( haplotigs ) )
     )
 }