From 0b40798d1b59a28bd86aa5b558a0793614be1efa Mon Sep 17 00:00:00 2001
From: Johnathan D <28043284+bjohnnyd@users.noreply.github.com>
Date: Mon, 19 Jul 2021 09:19:27 +0100
Subject: [PATCH] fix: lofreq/callparallel missing arg (#562) (#586)

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/lofreq/callparallel/main.nf        | 13 +++++++------
 modules/lofreq/callparallel/meta.yml       |  1 +
 tests/modules/lofreq/callparallel/test.yml |  9 +++++----
 3 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf
index 9ebb2805..4392c700 100644
--- a/modules/lofreq/callparallel/main.nf
+++ b/modules/lofreq/callparallel/main.nf
@@ -20,12 +20,12 @@ process LOFREQ_CALLPARALLEL {
 
     input:
     tuple val(meta), path(bam), path(bai)
-    file fasta
-    file fai
+    path fasta
+    path fai
 
     output:
-    tuple val(meta), path("*.vcf"), emit: vcf
-    path "*.version.txt"          , emit: version
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "*.version.txt"             , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -34,10 +34,11 @@ process LOFREQ_CALLPARALLEL {
     lofreq \\
         call-parallel \\
         --pp-threads $task.cpus \\
+        $options.args \\
         -f $fasta \\
-        -o ${prefix}.vcf \\
+        -o ${prefix}.vcf.gz \\
         $bam
 
-    echo \$(lofreq version 2>&1) | sed 's/^.*lofreq //; s/Using.*\$//' > ${software}.version.txt
+    echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//' > ${software}.version.txt
     """
 }
diff --git a/modules/lofreq/callparallel/meta.yml b/modules/lofreq/callparallel/meta.yml
index 43756e2b..3154f412 100644
--- a/modules/lofreq/callparallel/meta.yml
+++ b/modules/lofreq/callparallel/meta.yml
@@ -51,3 +51,4 @@ output:
 
 authors:
   - "@kaurravneet4123"
+  - "@bjohnnyd"
diff --git a/tests/modules/lofreq/callparallel/test.yml b/tests/modules/lofreq/callparallel/test.yml
index 3ffb459e..e09f68c3 100644
--- a/tests/modules/lofreq/callparallel/test.yml
+++ b/tests/modules/lofreq/callparallel/test.yml
@@ -1,7 +1,8 @@
-- name: lofreq callparallel
-  command: nextflow run ./tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c tests/config/nextflow.config
+- name: lofreq callparallel test_lofreq_callparallel
+  command: nextflow run tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c tests/config/nextflow.config
   tags:
-    - lofreq
     - lofreq/callparallel
+    - lofreq
   files:
-    - path: output/lofreq/test.vcf
+    - path: output/lofreq/test.vcf.gz
+      contains: ['##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">']