Merge branch 'master' into tool/elprep-merge

modules/elprep/filter/main.nf

@@ -23,7 +23,7 @@ process ELPREP_FILTER {
 
 
     output:
-    tuple val(meta), path("**.{bam,sam}")           ,emit: bam
+    tuple val(meta), path("output/**.{bam,sam}")    ,emit: bam
     tuple val(meta), path("*.metrics.txt")          ,optional: true, emit: metrics
     tuple val(meta), path("*.recall")               ,optional: true, emit: recall
     tuple val(meta), path("*.vcf.gz")               ,optional: true, emit: gvcf
@@ -65,7 +65,7 @@ process ELPREP_FILTER {
     def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
 
     """
-    elprep filter ${bam} ${prefix}.${suffix} \\
+    elprep filter ${bam} output/${prefix}.${suffix} \\
         ${reference_sequences_cmd} \\
         ${filter_regions_cmd} \\
         ${markdup_cmd} \\

modules/elprep/split/main.nf

@@ -11,16 +11,16 @@ process ELPREP_SPLIT {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("**.{bam,sam}"), emit: bam
+    tuple val(meta), path("output/**.{bam,sam}"), emit: bam
     path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    meta.single_end ? args += " --single-end": ""
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def single_end  = meta.single_end ? " --single-end": ""
 
     """
     # create directory and move all input so elprep can find and merge them before splitting
@@ -31,8 +31,9 @@ process ELPREP_SPLIT {
 
     elprep split \\
         input \\
-        . \\
+        output/ \\
         $args \\
+        $single_end \\
         --nr-of-threads $task.cpus \\
         --output-prefix $prefix
 

tests/modules/elprep/filter/test.yml

@@ -6,7 +6,7 @@
   files:
     - path: output/elprep/test.activity_profile.igv
     - path: output/elprep/test.assembly_regions.igv
-    - path: output/elprep/test.bam
+    - path: output/elprep/output/test.bam
     - path: output/elprep/test.g.vcf.gz
     - path: output/elprep/test.metrics.txt
     - path: output/elprep/test.recall

tests/modules/elprep/split/test.yml

@@ -4,7 +4,7 @@
     - elprep
     - elprep/split
   files:
-    - path: output/elprep/splits/test-group00001.bam
-    - path: output/elprep/splits/test-unmapped.bam
-    - path: output/elprep/test-spread.bam
+    - path: output/elprep/output/splits/test-group00001.bam
+    - path: output/elprep/output/splits/test-unmapped.bam
+    - path: output/elprep/output/test-spread.bam
     - path: output/elprep/versions.yml