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avoid bam2msa to create BAM index in inputdir #3986

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Merged
bgruening merged 3 commits into from
Sep 25, 2021
Merged

avoid bam2msa to create BAM index in inputdir #3986

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da571b2
avoid bam2msa to create BAM index in inputdir
pavanvidem Sep 24, 2021
4c56596
add input_bam in tool run
pavanvidem Sep 24, 2021
d8ef835
also link in index files
bgruening Sep 25, 2021
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5 changes: 4 additions & 1 deletion tools/bioext/bam2msa.xml
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Expand Up @@ -7,11 +7,14 @@
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
## avoid bam2msa to create .bai in inputdir
ln -s '$input' input_bam &&
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@bernt-matthias bernt-matthias Sep 24, 2021

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Galaxy already stores the index files (only for bam) and you can access it with:$input.metadata.bam_index. So ln -s '$input.metadata.bam_index' input_bam.bai may avoid that bam2msa needs to recreate it?

But I guess then we need a version bump.

ln -s '$input.metadata.bam_index' input_bam.bai &&
bam2msa
#if $region_start and $region_end:
-r $region_start:$region_end
#end if
'$input' '$output'
'input_bam' '$output'
]]></command>
<inputs>
<param name="input" type="data" format="bam,sam" label="Input BAM file"/>
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