Remove single_end if/else

software/minimap2/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+def options = initOptions(params.options)
 
 process MINIMAP2_ALIGN {
     tag "$meta.id"
@@ -24,33 +24,20 @@ process MINIMAP2_ALIGN {
 
     output:
     tuple val(meta), path("*.paf"), emit: paf
-    path "*.version.txt"          , emit: version
+    path "*.version.txt", emit: version
 
     script:
     def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    if (meta.single_end) {
-        """
-        minimap2 \\
-            $options.args \\
-            -t $task.cpus \\
-            $reference \\
-            $reads \\
-            > ${prefix}.paf
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    """
+    minimap2 \\
+        $options.args \\
+        -t $task.cpus \\
+        $reference \\
+        $input_reads \\
+        > ${prefix}.paf
 
-        echo \$(minimap2 --version 2>&1) > ${software}.version.txt
-        """
-    } else {
-        """
-        minimap2 \\
-            $options.args \\
-            -t $task.cpus \\
-            $reference \\
-            ${reads[0]} \\
-            ${reads[1]} \\
-            > ${prefix}.paf
-
-        echo \$(minimap2 --version 2>&1) > ${software}.version.txt
-        """
-    }
+    echo \$(minimap2 --version 2>&1) > ${software}.version.txt
+    """
 }

software/minimap2/align/meta.yml

@@ -43,8 +43,8 @@ input:
     - reads:
         type: file
         description: |
-            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-            respectively.
+            List of input FASTA or FASTQ files of size 1 and 2 for single-end
+            and paired-end data, respectively.
     - reference:
         type: file
         description: |

tests/software/minimap2/align/main.nf

@@ -24,14 +24,3 @@ workflow test_minimap2_align_paired_end {
                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
     MINIMAP2_ALIGN ( input, fasta )
 }
-
-workflow test_minimap2_align_pairwise {
-    
-    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
-
-    def input = []
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ fasta ] ]
-
-    MINIMAP2_ALIGN ( input, fasta )
-}