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Merge pull request #5 from UPHL-BioNGS/Tom_dev_231227
Tom dev 231227
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Original file line number | Diff line number | Diff line change |
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process VADR { | ||
tag "$meta.id" | ||
label 'process_medium' | ||
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container 'quay.io/staphb/vadr:1.6.3' | ||
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input: | ||
tuple val(meta), path(assembly) | ||
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output: | ||
tuple val(meta), path("${meta.id}/") , optional:true, emit: vadr | ||
path "*.vadr.log" , emit: log | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
def args2 = task.ext.args2 ?: "" | ||
def prefix = task.ext.prefix ?: "${meta.id}" | ||
def vadr_log = "${meta.id}.vadr.log" | ||
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""" | ||
fasta-trim-terminal-ambigs.pl \\ | ||
$args \\ | ||
$assembly > ${meta.id}.vadr_trimmed.fasta | ||
v-annotate.pl \\ | ||
$args2 \\ | ||
${meta.id}.vadr_trimmed.fasta \\ | ||
$meta.id | ||
# Soft link for traceability | ||
ln -s .command.log $vadr_log | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
vadr: \$(vadr --version 2>&1 | sed 's/^.*vadr //') | ||
END_VERSIONS | ||
""" | ||
} |
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