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mvdbeek
c0dbace7bb
This specifically addresses the problem where some jobs of a mapped-over collection have failed. Instead of filtering the failed collection and restarting the workflow at this position (involving a lot of copy-paste ...) the user can now limit the rerun to the problematic jobs and the workflow should resume from there. Should fix https://github.com/galaxyproject/galaxy/issues/2235. This is one possible implementation, it would also be feasible to not manipulate the original collection, but to copy the HDCA and then to replace collection elements and replace all references for jobs that depend on the HDCA, as we do for HDAs. This implementation seems simpler, but let me know if you see problems with this approach.
22 lines
686 B
XML
22 lines
686 B
XML
<tool id="fail_identifier" name="Fail input with identifier that contains fail">
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<command><![CDATA[
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#if $failbool and 'fail' in $input1.element_identifier
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sh -c "exit 127"
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#else
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cp '$input1' '$out_file1'
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#end if
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]]></command>
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<inputs>
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<param name="input1" type="data" label="An input file" />
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<param name="failbool" type="boolean" label="The failure property" checked="false" />
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</inputs>
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<outputs>
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<data name="out_file1" format="data"/>
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</outputs>
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<stdio>
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<exit_code range="127" level="fatal" description="Failing exit code." />
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</stdio>
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<help>
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</help>
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</tool>
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