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comparison flexbar_dsc.xml @ 30:3239487fa9c5 draft

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Uploaded
author rnateam
date Thu, 17 Dec 2015 11:19:35 -0500
parents 65103aba4e5f
children 7a1a5664a886
comparison
equal deleted inserted replaced
29:65103aba4e5f 30:3239487fa9c5
135 $cLogging.numTags 135 $cLogging.numTags
136 $cLogging.remTags 136 $cLogging.remTags
137 $cLogging.rndTags 137 $cLogging.rndTags
138 #end if 138 #end if
139 139
140 --target FlexbarOutput && 140 --target FlexbarOutput > $output &&
141 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done && 141 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`_forward.fastq"; done &&
142 for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done 142 for f in *_2.fastq; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq"; done
143 ]]></command> 143 ]]></command>
144 144
145 145
425 <!-- Use named regex group to grab pattern 425 <!-- Use named regex group to grab pattern
426 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list 426 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
427 identifier in the nested collection and identifier_1 is either 427 identifier in the nested collection and identifier_1 is either
428 forward or reverse (for instance samp1_forward.fq). 428 forward or reverse (for instance samp1_forward.fq).
429 --> 429 -->
430 <data format="txt" name="output" metadata_source="reads"/>
430 <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" /> 431 <discover_datasets pattern="FlexbarOutput_(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" metadata_source="reads" visible="true" />
431 <!--<data format="txt" name="output" metadata_source="reads"/>-->
432 </collection> 432 </collection>
433 </outputs> 433 </outputs>
434 434
435 435
436 <help> 436 <help>