added unaligned output

software/bowtie/align/main.nf

@@ -26,6 +26,8 @@ process BOWTIE_ALIGN {
     tuple val(meta), path('*.bam'), emit: bam
     tuple val(meta), path('*.out'), emit: log
     path  '*.version.txt'         , emit: version
+    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+    path 'test.txt', emit: test
 
     script:
     def software  = getSoftwareName(task.process)
@@ -45,6 +47,15 @@ process BOWTIE_ALIGN {
         2> ${prefix}.out \\
         | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
+    touch test.txt
+    if [ -f ${prefix}.unmapped.fastq ]; then
+        gzip ${prefix}.unmapped.fastq
+    fi
+    if [ -f ${prefix}.unmapped_1.fastq ]; then
+        gzip ${prefix}.unmapped_1.fastq
+        gzip ${prefix}.unmapped_2.fastq
+    fi
+
     echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
     """
 }

software/bowtie/align/meta.yml

@@ -53,13 +53,17 @@ input:
           description: Bowtie genome index files
           pattern: "*.ebwt"
 output:
-    - sam:
+    - bam:
           type: file
           description: Output SAM file containing read alignments
-        pattern: "*.{sam}"
+          pattern: "*.{bam}"
     - version:
           type: file
           description: File containing software version
           pattern: "*.{version.txt}"
+    - fastq:
+          type: file
+          description: Unaligned FastQ files
+          pattern: "*.fastq.gz"
 authors:
     - "@kevinmenden"