Whilst updating the yaml and its references I have come across a bug where the file isn't being renamed as expected, the string to represent the file location is however being changed. So CAT_CAT is outputting ${meta.id}.gz, the string representation is updated to ${meta.id}.fa.gz but the file is not updated, therefore causing FASTK_FASTK to error out.
I don't expect anything done so far to be negatively affected. As this is only an issue post yaml update (which is odd in and of itself).
To fix this, I have added some config for CAT_CAT that outputs a file named ${meta.id}_merged.fasta.gz which circumvents the renaming that was happening.
Description of the bug
Whilst updating the yaml and its references I have come across a bug where the file isn't being renamed as expected, the string to represent the file location is however being changed. So CAT_CAT is outputting
${meta.id}.gz, the string representation is updated to${meta.id}.fa.gzbut the file is not updated, therefore causing FASTK_FASTK to error out.I don't expect anything done so far to be negatively affected. As this is only an issue post yaml update (which is odd in and of itself).
To fix this, I have added some config for CAT_CAT that outputs a file named
${meta.id}_merged.fasta.gzwhich circumvents the renaming that was happening.Command used and terminal output
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Relevant files
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System information
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