Continuing the discussion from Batch export for files:
The useful script described previously seems to be incompatible with newer versions of qiime. The following line needs to be adapted -
qiime tools export ${i} --output-dir $output/${i}
because the currently used ‘input-path’ option will not accept
${i}
as an artifact.
Is there a solution or another way to batch export in newer qiime versions?
Hello @shira. What version of QIIME 2 are you using? In the latest versions, you will need to make that line qiime tools export --input-path ${i} --output-path $output/${i}