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Running a word count on a compressed fastq file now runs wc on the un… #4226

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Always

Just for now

@@ -12,11 +12,20 @@
echo "#${ "\t".join( [ i for i in $arg_order if i in $args ] ) }" > $out_file1
&&
#end if

##Handle compressed (fastq) input
#if $input1.is_of_type("fastq.gz"):
zcat $input1 |

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@nsoranzo

nsoranzo Jun 26, 2017

Member

Single-quote $input1 here and below?

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@dpryan79

dpryan79 Jun 26, 2017

Author Contributor

Yes, thanks for catching this!

#else if $input1.is_of_type("fastq.bz2"):
bzcat $input1 |
#else:
cat $input1 |
#end if
wc
#for $option in $args:
-${ word_to_arg[ str(option) ] }
#end for
$input1 | awk '{ print ${ '"\\t"'.join( [ "$%i" % ( i+1 ) for i in range( len( $args ) ) ] ) } }'
| awk '{ print ${ '"\\t"'.join( [ "$%i" % ( i+1 ) for i in range( len( $args ) ) ] ) } }'
>> $out_file1
</command>
<inputs>
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