Enable Galaxy outputs_to_working_directory by default
#1199
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most importantly this will set the galaxy dir and its files dir to read only. which allows planemo test to find cases of tools that write into galaxy's files dir. see also here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483
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nsoranzo
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May 16, 2022
nsoranzo
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outputs_to_working_directory by default
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because a .fai is written next to it leads to a failing ci job due to galaxyproject/planemo#1199
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* allow 4 diff for bam files an additional diff line is due to more processors used xref #4490 * link fasta file because a .fai is written next to it leads to a failing ci job due to galaxyproject/planemo#1199
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most importantly this will set the galaxy dir and its files dir to read only (for dockerized testing). which allows planemo test to find cases of tools that write into galaxy's files dir.
see also here https://github.com/galaxyproject/galaxy/blob/5dc9111f45b4ed5012575b31e199a591cfad6d7a/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L483
related: #1190