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Commit 8715adec authored by Jelle Scholtalbers's avatar Jelle Scholtalbers :flag_nl:
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keep source format; divide slots by 2 for each pigz process

parent d01b2bc0
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......@@ -6,7 +6,7 @@
#if not $compress:
zcat $input | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $read1) | cut -f 5-8 | tr "\t" "\n" > $read2
#else:
zcat $input | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes "\${GALAXY_SLOTS/2:-4}" > $read1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes "\${GALAXY_SLOTS/2:-4}" > $read2
zcat $input | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes "\$((\${GALAXY_SLOTS:-4}/2))" > $read1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes "\$((\${GALAXY_SLOTS:-4}/2))" > $read2
#end if
]]></command>
<inputs>
......@@ -15,8 +15,8 @@
</inputs>
<outputs>
<data name="read1" format="fastq" label="Read1"/>
<data name="read2" format="fastq" label="Read2"/>
<data name="read1" format_source="input" label="${tool.name} on ${on_string}: Read1"/>
<data name="read2" format_source="input" label="${tool.name} on ${on_string}: Read2"/>
</outputs>
<tests>
......
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