bowtie bam output

software/bowtie/align/main.nf

@@ -11,15 +11,15 @@ process BOWTIE_ALIGN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda     (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
-    container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
+    conda     (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
+    container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
 
     input:
     tuple val(meta), path(reads)
     path  index
     
     output:
-    tuple val(meta), path("*.sam"), emit: sam
+    tuple val(meta), path("*.bam"), emit: bam
     tuple val(meta), path("*.out"), emit: log
     path  "bowtie.version.txt", emit: version
 
@@ -27,15 +27,19 @@ process BOWTIE_ALIGN {
     def software  = getSoftwareName(task.process)
     def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : ''
+    def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     """
     INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
     bowtie \\
         --threads $task.cpus \\
-        $options.args \\
-        \$INDEX \\
-        -q ${reads} \\
+        --sam \\
+        -x \$INDEX \\
+        -q \\
 	    $unaligned \\
-	> ${prefix}.sam 2> ${prefix}.out
+        $options.args \\
+        $endedness \\
+	    2> ${prefix}.out \\
+        | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
     bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt
     """

tests/software/bowtie/main.nf

@@ -5,8 +5,6 @@ nextflow.enable.dsl = 2
 include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
 include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf'  addParams( options: [:] )
 
-
-
 workflow test_bowtie_index {
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
     BOWTIE_INDEX ( fasta ) 
@@ -19,7 +17,7 @@ workflow test_bowtie_alignment_single_end {
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 
@@ -29,8 +27,8 @@ workflow test_bowtie_alignment_paired_end {
 
     def input = []
     input = [ [ id:'test', single_end:false ], // meta map
-              [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
-                file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
+              [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 

tests/software/bowtie/test.yml

@@ -36,9 +36,9 @@
     - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
-      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
-    - path: output/bowtie/test.sam
-      md5sum: acdb36ea915ac2ac71b69a0b704d9d8a
+      md5sum: a81cb18024616415a6cec3108a36fccd
+    - path: output/bowtie/test.bam
+      md5sum: 8179c68a819accbc9137dc881736106f
 
 
 - name: Run bowtie index and align paired_end
@@ -60,7 +60,7 @@
     - path: output/bowtie/bowtie/NC_010473.index.rev.2.ebwt
       md5sum: f3c398bba5158f4039334a932d79c051
     - path: output/bowtie/test.out
-      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
-    - path: output/bowtie/test.sam
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+      md5sum: a23e9a2a76e949aeb3693bcfae41a615
+    - path: output/bowtie/test.bam
+      md5sum: 9ce5aebf37128f4bb1d24e9548e22009