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Remove ref to conda build and additional params

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Anders Goncalves da Silva 2021-02-12 14:43:50 -08:00
parent ffc849761d
commit b08bf1ea5c
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1 changed files with 4 additions and 12 deletions
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software/ivar/consensus/main.nf
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@ -11,7 +11,7 @@ process IVAR_CONSENSUS {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::ivar=1.3.1=h089eab3_0" : null) conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0" container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
} else { } else {
@ -31,20 +31,12 @@ process IVAR_CONSENSUS {
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def save_mpileup = options.save_mpileup ? "tee ${prefix}.mpileup |" : "" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
def min_bq = options.min_bq ? "-Q ${options.min_bq}" : "-Q 0"
def max_depth = options.max_depth ? "-d ${options.max_depth}" : "-d 0"
def count_orphans = options.count_orphans ? "-A" : ""
def disable_baq = options.disable_baq ? "-B" : ""
def output_all_bases = options.output_all_bases ? "-aa" : ""
""" """
samtools mpileup \\ samtools mpileup \\
--fasta-ref $fasta \\ --fasta-ref $fasta \\
$output_all_bases \\ -aa \\
$count_orphans \\
$disable_baq \\
$max_depth \\
$min_bq \\
$options.args2 \\ $options.args2 \\
$bam | \\ $bam | \\
$save_mpileup \\ $save_mpileup \\