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Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline
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Fix: Add overwriting of destination #84

Closed ingkebil closed 3 years ago

ingkebil commented 5 years ago

This PR fixes the jobs failing when the output directory Unaligned already exists.

How to test:

  1. Install branch with update script on stage
  2. run: rm /home/proj/stage/flowcells/hiseqx/170630_ST-E00198_0227_AH2GL2CCXY/demuxstarted.txt
  3. run: bash ${PROJECT_HOME}/stage/bin/git/demultiplexing/scripts/hiseqx/xcheckfornewrun.bash ${PROJECT_HOME}/stage/flowcells/hiseqx/ ${PROJECT_HOME}/stage/demultiplexed-runs/

... aaaha ran out of time!

henrikstranneheim commented 3 years ago

@barrystokman Is this still relevant?

barrystokman commented 3 years ago

In some cases this could be useful, for instance re-demultiplexing FCs for which the project dirs in Unaligned already exist

edit: currently, removing the unaligned dir is a manual action, adding 20 seconds of work max.

henrikstranneheim commented 3 years ago

@barrystokman and @karlnyr Merge or close?

barrystokman commented 3 years ago

@karlnyr your call

karlnyr commented 3 years ago

I feel like this is the wrong way to do it. Better to clean target directory on restart than copying over newly added files. The one situation where this could be slightly useful is for mixed samplesheet runs, but even then I feel like this is not the most safe way to do it. In other words, CLOSE!