pipeline does not work if analysis directory is moved about sns HOT 6 CLOSED

You shouldn't change directories. For safety, everything is based on absolute paths.

Sample-related file paths are in the samples.*.csv files.

from sns.

this makes the results un-portable and the pipeline non-reproducible, since it will no longer run if it is not in its original location.

from sns.

from sns.

It can be ported and reproduced in a new location.

Most software tools fail if interrupted in the middle of a run.

from sns.

This is independent of have tools running.

Here is the workflow that produced this error:

• setup and run initial sns analysis: sns/run wes

• run paired variant calling analysis: sns/run wes-pairs-snv

• all sns jobs completed

• moved the analysis directory for collaboration & working on CNV analysis

• tried to run the CNV analysis: sns/run wes-pairs-cnv

• errors as described here

How can it be 'reproduced in a new location' if you can no longer run the pipeline in a new location? Considering that it usually takes 24-48 hours to run both wes and wes-pairs-snv routes, having to start the entire analysis from scratch just for the sake of wanting to move the parent analysis directory to a different location does not seem ideal.

from sns.

You moved the directory before the analysis was finished. Do not move the directory in the middle of analysis.

Semantics aside, the workaround is to modify the samples.*.csv files where sample-related file paths are stored.

from sns.