From 98b024c0e46ef0ea994cd2cba408f0043e7e4dcf Mon Sep 17 00:00:00 2001
From: "Maxime U. Garcia" <max.u.garcia@gmail.com>
Date: Mon, 6 Dec 2021 12:59:49 +0100
Subject: [PATCH] Fix syntax for extra containers for ensemblvep and snpeff
 (#1105)

* fix: correct syntax for task.ext.use_cache

* Apply suggestions from code review

* fix: simplify logic

* fix: update to new syntax
---
 modules/ensemblvep/main.nf               | 14 ++++++--------
 modules/snpeff/main.nf                   | 14 ++++++--------
 tests/modules/ensemblvep/nextflow.config |  3 +--
 tests/modules/snpeff/nextflow.config     |  3 +--
 4 files changed, 14 insertions(+), 20 deletions(-)

diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf
index 3182feb2..9caffb0c 100644
--- a/modules/ensemblvep/main.nf
+++ b/modules/ensemblvep/main.nf
@@ -2,13 +2,11 @@ process ENSEMBLVEP {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null)
-    if (task.ext.use_cache) {
-        container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        !task.ext.container_tag ?
             'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' :
-            'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }"
-    } else {
-        container "nfcore/vep:${task.ext.vep_tag}"
-    }
+            'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' :
+            "nfcore/vep:${task.ext.container_tag}" }"
 
     input:
     tuple val(meta), path(vcf)
@@ -25,7 +23,7 @@ process ENSEMBLVEP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def dir_cache = task.ext.use_cache ? "\${PWD}/${cache}" : "/.vep"
+    def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
     """
     mkdir $prefix
 
@@ -39,7 +37,7 @@ process ENSEMBLVEP {
         --cache_version $cache_version \\
         --dir_cache $dir_cache \\
         --fork $task.cpus \\
-        --format vcf \\
+        --vcf \\
         --stats_file ${prefix}.summary.html
 
     rm -rf $prefix
diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf
index d0ec993e..db9cca72 100644
--- a/modules/snpeff/main.nf
+++ b/modules/snpeff/main.nf
@@ -2,13 +2,11 @@ process SNPEFF {
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
-    if (task.ext.use_cache) {
-        container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        !task.ext.container_tag ?
             'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
-            'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
-    } else {
-        container "nfcore/snpeff:${task.ext.snpeff_tag}"
-    }
+            'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' :
+            "nfcore/snpeff:${task.ext.container_tag}" }"
 
     input:
     tuple val(meta), path(vcf)
@@ -29,14 +27,14 @@ process SNPEFF {
         avail_mem = task.memory.giga
     }
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def dir_cache = task.ext.use_cache ? "-dataDir \${PWD}/${cache}" : ""
+    def cache_command = cache ? "-dataDir \${PWD}/${cache}" : ""
     """
     snpEff \\
         -Xmx${avail_mem}g \\
         $db \\
         $args \\
         -csvStats ${prefix}.csv \\
-        $dir_cache \\
+        $cache_command \\
         $vcf \\
         > ${prefix}.ann.vcf
 
diff --git a/tests/modules/ensemblvep/nextflow.config b/tests/modules/ensemblvep/nextflow.config
index bcca2d06..717fcae9 100644
--- a/tests/modules/ensemblvep/nextflow.config
+++ b/tests/modules/ensemblvep/nextflow.config
@@ -3,8 +3,7 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: ENSEMBLVEP {
-        ext.vep_tag = '104.3.WBcel235'
-        ext.use_cache = false
+        ext.container_tag = '104.3.WBcel235'
     }
 
 }
diff --git a/tests/modules/snpeff/nextflow.config b/tests/modules/snpeff/nextflow.config
index 589c8cfb..3b094eed 100644
--- a/tests/modules/snpeff/nextflow.config
+++ b/tests/modules/snpeff/nextflow.config
@@ -3,8 +3,7 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: SNPEFF {
-        ext.snpeff_tag = '5.0.WBcel235'
-        ext.use_cache = false
+        ext.container_tag = '5.0.WBcel235'
     }
 
 }