create optional cleanup script, especially for reporting.

[colindaven]

• reporting
• bams?
• rm fastqs
• gzip R1.fastq
• reduce no of files
• [ ]

[LisaHollstein]

Is this still needed? I could write something for this

[colindaven]

Yes, I just committed what I have to dev.

Further ideas:

• remove big files in raspir subdir
• old reporting files are not used if haybaler output folders are filled - so can be deleted. Ie. noone looks at reporting, just haybaler : STOP - we need the reporting files for code report integration, as one sample per file, whereas haybaler has many samples per file.
• in plots, multiple image folders are created. Could delete old image subfolders (run plots many times to test)
• ...

[LisaHollstein]

I just noticed an error in wochenende_cleanup.sh:

base_dir=$(pwd)
echo $base_dir

echo "INFO: removing png files from growth_rate"
# a find exec rm is dangerous though, so go more targeted
cd growth_rate
#find . -n
cd $bash_dir

A variable bash_dir is never declared, this should probably mean base_dir, which is declared at the beginning of the script.

[colindaven]

True, ups, will correct and add a pipefail statement.

[colindaven]

I used
set -u pipefail
to check for unused variables.

See https://vaneyckt.io/posts/safer_bash_scripts_with_set_euxo_pipefail/