From bf91f9dd9b62c98175d962bd51dbe2d0b7f91d4c Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Mon, 9 May 2022 14:54:52 +0200
Subject: [PATCH] update arriba module

---
 modules/arriba/main.nf  | 32 ++++++++++++++++++++++++++++----
 modules/arriba/meta.yml | 22 +++++++++++++++++++++-
 2 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/modules/arriba/main.nf b/modules/arriba/main.nf
index e0d30b45..b7883acd 100644
--- a/modules/arriba/main.nf
+++ b/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' :
-        'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
+        'https://depot.galaxyproject.org/singularity/arriba:2.2.1--hecb563c_2' :
+        '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
+    """
 }
diff --git a/modules/arriba/meta.yml b/modules/arriba/meta.yml
index 4bde2f08..119dd912 100644
--- a/modules/arriba/meta.yml
+++ b/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"