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hifiasm2 allow excluding --primary #6484

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hifiasm2 allow excluding --primary #6484

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2683c91
allow excluding --primary
alpapan Oct 23, 2024
2ca4cd0
bump hifiasm version
alpapan Oct 23, 2024
b9bee22
patch3 hifiasm.xml
alpapan Oct 24, 2024
fecdcaf
fix lint errors
alpapan Oct 24, 2024
0f5407a
minor remnant
alpapan Oct 24, 2024
6e1b558
whitespace
alpapan Oct 24, 2024
505d955
remove comment
alpapan Oct 24, 2024
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7 changes: 5 additions & 2 deletions tools/hifiasm/hifiasm.xml
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Expand Up @@ -162,9 +162,11 @@
--ul-tip $ont_integration.ul_tip
#end if
#end if

#if $assembly_options.primary
--primary
#end if

## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
--primary
$input_filenames
#if $log_out:
2> output.log
Expand Down Expand Up @@ -216,6 +218,7 @@
</param>
<when value="blank"/>
<when value="set">
<param name="primary" type="boolean" truevalue="--primary" falsevalue="" checked="true" label="Create primary and alternate assemblies" help="Hifiasm outputs a primary assembly and two balanced haplotypes by default. This will output a primary assembly and alternate assembly only (--primary)."/>
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Suggested change
<param name="primary" type="boolean" truevalue="--primary" falsevalue="" checked="true" label="Create primary and alternate assemblies" help="Hifiasm outputs a primary assembly and two balanced haplotypes by default. This will output a primary assembly and alternate assembly only (--primary)."/>
<param argument="--primary" type="boolean" truevalue="--primary" falsevalue="" checked="true" label="Create primary and alternate assemblies" help="Hifiasm outputs a primary assembly and two balanced haplotypes by default. This will output a primary assembly and alternate assembly only"/>

<param name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds"/>
<param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed"/>
<param name="pop_contigs" argument="-m" type="integer" value="10000000" label="Minimum contig bubble size" help="Pop contig graph bubbles smaller than this value"/>
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