mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-09-21 05:32:05 +00:00
chore: update krakenuniq
This commit is contained in:
Moritz E. Beber
parent
ddcf38de22
commit
af8ce2cbfd
3 changed files with 182 additions and 75 deletions
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@ -99,7 +99,7 @@
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},
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"krakenuniq/preloadedkrakenuniq": {
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"branch": "master",
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"git_sha": "13b9d4854593c03e5e25e8a8f47462542c2c0dd4"
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"git_sha": "05649975c6611c6e007537a7984e186e12ae03af"
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},
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"krona/ktimporttaxonomy": {
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"branch": "master",
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248
modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
generated
248
modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
generated
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@ -1,4 +1,5 @@
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process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::krakenuniq=1.0.0" : null)
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@ -29,90 +30,195 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
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def args = task.ext.args ?: ''
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def args2 = task.ext.args ?: ''
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def paired = meta.single_end ? "" : "--paired"
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def classified = meta.single_end ? '"\$PREFIX".classified.fastq' : '"\$PREFIX".classified#.fastq'
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def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
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def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
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def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
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def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
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def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
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def compress_reads_command = save_output_fastqs ? "gzip --no-name *.fastq" : ""
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"""
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krakenuniq \\
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$args \\
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--db $db \\
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--preload $ram_chunk_size \\
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--threads $task.cpus
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# for fastq in "${fastqs.join('\" \"')}"; do \\
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for fastq in ${fastqs}; do \\
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PREFIX=\$(echo \$fastq)
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def classified = meta.single_end ? '"\${PREFIX}.classified.fastq"' : '"\${PREFIX}.classified#.fastq"'
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def unclassified = meta.single_end ? '"\${PREFIX}.unclassified.fastq"' : '"\${PREFIX}.unclassified#.fastq"'
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def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ''
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def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ''
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def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
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def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
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def compress_reads_command = save_output_fastqs ? 'gzip --no-name *.fastq' : ''
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if (meta.single_end) {
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"""
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krakenuniq \\
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--db $db \\
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--preload \\
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--preload-size $ram_chunk_size \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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$paired \\
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$args2 \\
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\$fastq
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done
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$args
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$compress_reads_command
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strip_suffix() {
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local result=\$1
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# Strip any file extensions.
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echo "\${result%%.*}"
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}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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printf "%s\\n" ${fastqs} | while read FASTQ; do \\
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PREFIX="\$(strip_suffix "\${FASTQ}")"
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krakenuniq \\
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--db $db \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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$args2 \\
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"\${FASTQ}"
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done
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$compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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krakenuniq \\
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--db $db \\
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--preload \\
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--preload-size $ram_chunk_size \\
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--threads $task.cpus \\
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$args
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strip_suffix() {
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local result
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read result
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# Strip any trailing dot or underscore.
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result="\${result%_}"
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echo "\${result%.}"
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}
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printf "%s %s\\n" ${fastqs} | while read FASTQ; do \\
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read -r -a FASTQ <<< "\${FASTQ}"
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PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
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krakenuniq \\
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--db $db \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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--paired \\
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$args2 \\
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"\${FASTQ[@]}"
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done
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$compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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stub:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args ?: ''
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def paired = meta.single_end ? "" : "--paired"
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def classified = meta.single_end ? '"\$PREFIX".classified.fastq' : '"\$PREFIX".classified#.fastq'
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def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
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def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
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def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
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def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
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def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
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def compress_reads_command = save_output_fastqs ? "echo 'gzip --no-name *.fastq'" : ""
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"""
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echo "krakenuniq \\
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$args \\
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--db $db \\
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--preload $ram_chunk_size \\
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--threads $task.cpus"
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for fastq in "${fastqs.join('\" \"')}"; do \\
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PREFIX=\$(echo \$fastq)
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echo "krakenuniq \\
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def classified = meta.single_end ? '"\${PREFIX}.classified.fastq"' : '"\${PREFIX}.classified#.fastq"'
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def unclassified = meta.single_end ? '"\${PREFIX}.unclassified.fastq"' : '"\${PREFIX}.unclassified#.fastq"'
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def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ''
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def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ''
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def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
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def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
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def compress_reads_command = save_output_fastqs ? 'gzip --no-name *.fastq' : ''
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if (meta.single_end) {
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"""
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echo krakenuniq \\
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--db $db \\
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--preload \\
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--preload-size $ram_chunk_size \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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$paired \\
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$args2 \\
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\$fastq"
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$args
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touch "\$PREFIX".classified.fastq.gz
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touch "\$PREFIX".krakenuniq.classified.txt
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touch "\$PREFIX".krakenuniq.report.txt
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touch "\$PREFIX".unclassified.fastq.gz
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done
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strip_suffix() {
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local result=\$1
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# Strip any file extensions.
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echo "\${result%%.*}"
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}
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$compress_reads_command
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printf "%s\\n" ${fastqs} | while read FASTQ; do \\
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echo "\${FASTQ}"
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PREFIX="\$(strip_suffix "\${FASTQ}")"
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echo "\${PREFIX}"
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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echo krakenuniq \\
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--db $db \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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$args2 \\
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"\${FASTQ}"
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touch "\${PREFIX}.classified.fastq.gz"
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touch "\${PREFIX}.krakenuniq.classified.txt"
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touch "\${PREFIX}.krakenuniq.report.txt"
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touch "\${PREFIX}.unclassified.fastq.gz"
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done
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echo $compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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echo krakenuniq \\
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--db $db \\
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--preload \\
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--preload-size $ram_chunk_size \\
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--threads $task.cpus \\
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$args
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strip_suffix() {
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local result
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read result
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# Strip any trailing dot or underscore.
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result="\${result%_}"
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echo "\${result%.}"
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}
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printf "%s %s\\n" ${fastqs} | while read FASTQ; do \\
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read -r -a FASTQ <<< "\${FASTQ}"
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echo "\${FASTQ[@]}"
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PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
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echo "\${PREFIX}"
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echo krakenuniq \\
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--db $db \\
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--threads $task.cpus \\
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$report \\
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$output_option \\
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$unclassified_option \\
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$classified_option \\
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$output_option \\
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--paired \\
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$args2 \\
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"\${FASTQ[@]}"
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touch "\${PREFIX}.classified_1.fastq.gz" "\${PREFIX}.classified_2.fastq.gz"
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touch "\${PREFIX}.krakenuniq.classified.txt"
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touch "\${PREFIX}.krakenuniq.report.txt"
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touch "\${PREFIX}.unclassified_1.fastq.gz" "\${PREFIX}.unclassified_2.fastq.gz"
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done
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echo $compress_reads_command
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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}
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@ -51,13 +51,13 @@ output:
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description: |
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Reads classified as belonging to any of the taxa
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on the KrakenUniq database.
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pattern: "*{fastq.gz}"
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pattern: "*.fastq.gz"
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- unclassified_reads_fastq:
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type: file
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description: |
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Reads not classified to any of the taxa
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on the KrakenUniq database.
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pattern: "*{fastq.gz}"
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pattern: "*.fastq.gz"
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- classified_assignment:
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type: file
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description: |
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@ -68,10 +68,11 @@ output:
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description: |
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KrakenUniq report containing stats about classified
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and not classifed reads.
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pattern: "*.{report.txt}"
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pattern: "*.report.txt"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@mjamy"
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- "@Midnighter"
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