Merge pull request #1638 from rannick/master

Update arriba

modules/arriba/main.nf

@@ -2,15 +2,20 @@ process ARRIBA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::arriba=2.1.0" : null)
+    conda (params.enable_conda ? "bioconda::arriba=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1' :
+        'https://depot.galaxyproject.org/singularity/arriba:2.2.1--hecb563c_2' :
-        'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
+        'quay.io/biocontainers/arriba:2.2.1--hecb563c_2' }"
 
     input:
     tuple val(meta), path(bam)
     path fasta
     path gtf
+    path blacklist
+    path known_fusions
+    path structural_variants
+    path tags
+    path protein_domains
 
     output:
     tuple val(meta), path("*.fusions.tsv")          , emit: fusions
@@ -23,7 +28,12 @@ process ARRIBA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def blacklist = (args.contains('-b')) ? '' : '-f blacklist'
+    def blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
+    def known_fusions = known_fusions ? "-k $known_fusions" : ""
+    def structural_variants = structural_variants ? "-d $structual_variants" : ""
+    def tags = tags ? "-t $tags" : ""
+    def protein_domains = protein_domains ? "-p $protein_domains" : ""
+
     """
     arriba \\
         -x $bam \\
@@ -32,6 +42,10 @@ process ARRIBA {
         -o ${prefix}.fusions.tsv \\
         -O ${prefix}.fusions.discarded.tsv \\
         $blacklist \\
+        $known_fusions \\
+        $structural_variants \\
+        $tags \\
+        $protein_domains \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -39,4 +53,14 @@ process ARRIBA {
         arriba: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo stub > ${prefix}.fusions.tsv
+    echo stub > ${prefix}.fusions.discarded.tsv
+
+    echo "${task.process}:" > versions.yml
+    echo ' arriba: 2.2.1' >> versions.yml
+    """
 }

modules/arriba/meta.yml

@@ -30,6 +30,26 @@ input:
       type: file
       description: Annotation GTF file
       pattern: "*.{gtf}"
+  - blacklist:
+      type: file
+      description: Blacklist file
+      pattern: "*.{tsv}"
+  - known_fusions:
+      type: file
+      description: Known fusions file
+      pattern: "*.{tsv}"
+  - structural_variants:
+      type: file
+      description: Structural variants file
+      pattern: "*.{tsv}"
+  - tags:
+      type: file
+      description: Tags file
+      pattern: "*.{tsv}"
+  - protein_domains:
+      type: file
+      description: Protein domains file
+      pattern: "*.{gff3}"
 
 output:
   - meta:
@@ -51,4 +71,4 @@ output:
       pattern: "*.{fusions.discarded.tsv}"
 
 authors:
-  - "@praveenraj2018"
+  - "@praveenraj2018,@rannick"

tests/modules/arriba/main.nf

@@ -20,7 +20,7 @@ workflow test_arriba_single_end {
 
     STAR_GENOMEGENERATE ( fasta, gtf )
     STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
+    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [], [], [], [], [])
 }
 
 workflow test_arriba_paired_end {
@@ -38,5 +38,5 @@ workflow test_arriba_paired_end {
 
     STAR_GENOMEGENERATE ( fasta, gtf )
     STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
+    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [], [], [], [], [])
 }

tests/modules/arriba/test.yml

@@ -4,7 +4,7 @@
     - arriba
   files:
     - path: output/arriba/test.fusions.discarded.tsv
-      md5sum: cad8c215b938d1e45b747a5b7898a4c2
+      md5sum: 7602ab4ccbbb0c54fbca12a942877e6d
     - path: output/arriba/test.fusions.tsv
       md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
     - path: output/star/star/Genome
@@ -39,6 +39,7 @@
     - path: output/star/star/transcriptInfo.tab
       md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
     - path: output/star/test.Aligned.out.bam
+      md5sum: 4fa079d11f8938e51015e3e477fa7149
     - path: output/star/test.Log.final.out
     - path: output/star/test.Log.out
     - path: output/star/test.Log.progress.out
@@ -50,7 +51,7 @@
     - arriba
   files:
     - path: output/arriba/test.fusions.discarded.tsv
-      md5sum: 85e36c887464e4deaa65f45174d3b8fd
+      md5sum: cdc6cfbc75e68ce29a766f50f390274d
     - path: output/arriba/test.fusions.tsv
       md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
     - path: output/star/star/Genome