Merge pull request #122 from CDCgov/snpEff_fix

Remove snpEff logging

modules/local/snpeff_ann.nf

@@ -37,6 +37,7 @@ process SNPEFF_ANN {
     snpEff \\
         -Xmx${avail_mem}g \\
         ${fasta.baseName} \\
+        -noLog \\
         -config $config \\
         -dataDir $db \\
         $args \\
@@ -47,7 +48,7 @@ process SNPEFF_ANN {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        snpeff: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
+        snpeff: \$(echo \$(snpEff -noLog -version 2>&1) | cut -f 2 -d ' ')
     END_VERSIONS
     """
 }

modules/local/snpeff_build.nf

@@ -44,6 +44,7 @@ process SNPEFF_BUILD {
     snpEff \\
         -Xmx${avail_mem}g \\
         build \\
+        -noLog \\
         -config snpeff.config \\
         -dataDir ./snpeff_db \\
         -gff3 \\
@@ -52,7 +53,7 @@ process SNPEFF_BUILD {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        snpeff: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
+        snpeff: \$(echo \$(snpEff -noLog -version 2>&1) | cut -f 2 -d ' ')
     END_VERSIONS
     """
 }

modules/local/snpeff_local.nf

@@ -1,47 +1,48 @@
-process SNPEFF {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::snpeff=4.3" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/snpeff:4.3.1t--hdfd78af_5' :
-        'quay.io/biocontainers/snpeff:4.3.1t--hdfd78af_5' }"
-
-    input:
-    tuple val(meta), path(vcf)
-    val species
-
-    output:
-    tuple val(meta), path("*.ann.vcf"), emit: vcf
-    path "*.csv"                      , emit: report
-    path "*.html"                     , emit: summary_html
-    path "*.genes.txt"                , emit: genes_txt
-    path "versions.yml"               , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def avail_mem = 6
-    if (!task.memory) {
-        log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
-    } else {
-        avail_mem = task.memory.giga
-    }
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    snpEff \\
-        -Xmx${avail_mem}g \\
-        $args \\
-        -v $species \\
-        -csvStats ${prefix}.csv \\
-        $vcf \\
-        > ${prefix}.ann.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        snpeff: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
-    END_VERSIONS
-    """
-}
+process SNPEFF {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::snpeff=4.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/snpeff:4.3.1t--hdfd78af_5' :
+        'quay.io/biocontainers/snpeff:4.3.1t--hdfd78af_5' }"
+
+    input:
+    tuple val(meta), path(vcf)
+    val species
+
+    output:
+    tuple val(meta), path("*.ann.vcf"), emit: vcf
+    path "*.csv"                      , emit: report
+    path "*.html"                     , emit: summary_html
+    path "*.genes.txt"                , emit: genes_txt
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def avail_mem = 6
+    if (!task.memory) {
+        log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    snpEff \\
+        -Xmx${avail_mem}g \\
+        $args \\
+        -noLog \\
+        -v $species \\
+        -csvStats ${prefix}.csv \\
+        $vcf \\
+        > ${prefix}.ann.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snpeff: \$(echo \$(snpEff -noLog -version 2>&1) | cut -f 2 -d ' ')
+    END_VERSIONS
+    """
+}