Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile

modules/filtlong/main.nf

@@ -11,7 +11,7 @@ process FILTLONG {
     tuple val(meta), path(shortreads), path(longreads)
 
     output:
-    tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
     path "versions.yml"                                     , emit: versions
 
     when:
@@ -21,12 +21,13 @@ process FILTLONG {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
+    if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     filtlong \\
         $short_reads \\
         $args \\
         $longreads \\
-        | gzip -n > ${prefix}_lr_filtlong.fastq.gz
+        | gzip -n > ${prefix}.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/gatk4/mergevcfs/main.nf

@@ -13,6 +13,7 @@ process GATK4_MERGEVCFS {
 
     output:
     tuple val(meta), path('*.vcf.gz'), emit: vcf
+    tuple val(meta), path("*.tbi")   , emit: tbi
     path  "versions.yml"             , emit: versions
 
     when:

modules/gatk4/mergevcfs/meta.yml

@@ -35,6 +35,11 @@ output:
       type: file
       description: merged vcf file
       pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: index files for the merged vcf files
+      pattern: "*.tbi"
+
   - versions:
       type: file
       description: File containing software versions

tests/modules/filtlong/nextflow.config

@@ -3,5 +3,6 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     ext.args = "--min_length 10"
+    ext.prefix = "test_lr"
 
 }

tests/modules/filtlong/test.yml

@@ -3,7 +3,7 @@
   tags:
     - filtlong
   files:
-    - path: output/filtlong/test_lr_filtlong.fastq.gz
+    - path: output/filtlong/test_lr.fastq.gz
       contains:
         - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
@@ -12,7 +12,7 @@
   tags:
     - filtlong
   files:
-    - path: output/filtlong/test_lr_filtlong.fastq.gz
+    - path: output/filtlong/test_lr.fastq.gz
       contains:
         - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
@@ -21,6 +21,6 @@
   tags:
     - filtlong
   files:
-    - path: output/filtlong/test_lr_filtlong.fastq.gz
+    - path: output/filtlong/test_lr.fastq.gz
       contains:
         - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"

tests/modules/gatk4/mergevcfs/test.yml

@@ -6,6 +6,8 @@
   files:
     - path: output/gatk4/test.vcf.gz
       md5sum: 5b289bda88d3a3504f2e19ee8cff177c
+    - path: output/gatk4/test.vcf.gz.tbi
+      md5sum: a81673763b13086cfce9a23e72a35a16
     - path: output/gatk4/versions.yml
 
 - name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict