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edna
snakemake_rapidrun_obitools
Commits
6a5603c3
Commit
6a5603c3
authored
Jul 27, 2020
by
peguerin
Browse files
script to clean outputs
parent
34141842
Changes
1
Hide whitespace changes
Inline
Side-by-side
clean.sh
0 → 100644
View file @
6a5603c3
###############################################################################
MODE
=
$1
if
[
-d
"results"
]
;
then
if
[
"
$MODE
"
==
"clear"
]
;
then
echo
-n
"Clearing..."
mv
-i
results cleared/
mkdir
results
mkdir
results/01_settings results/02_assembly results/03_demultiplex results/04_filter_samples results/05_assignment results/06_final_tables
mkdir
results/02_assembly/01_illuminapairedend results/02_assembly/02_remove_unaligned
mkdir
results/03_demultiplex/00_dat results/03_demultiplex/01_assign_sequences results/03_demultiplex/02_raw
mkdir
results/04_filter_samples/01_dereplicated results/04_filter_samples/02_goodlength results/04_filter_samples/03_clean_pcrerr results/04_filter_samples/04_filtered
mkdir
results/05_assignment/01_runs results/05_assignment/02_dereplicated results/05_assignment/03_assigned results/05_assignment/04_formated
echo
"done"
elif
[
"
$MODE
"
==
"reset"
]
;
then
echo
-n
"Resetting..."
rm
-r
results
mkdir
results
mkdir
results/01_settings results/02_assembly results/03_demultiplex results/04_filter_samples results/05_assignment results/06_final_tables
mkdir
results/02_assembly/01_illuminapairedend results/02_assembly/02_remove_unaligned
mkdir
results/03_demultiplex/00_dat results/03_demultiplex/01_assign_sequences results/03_demultiplex/02_raw
mkdir
results/04_filter_samples/01_dereplicated results/04_filter_samples/02_goodlength results/04_filter_samples/03_clean_pcrerr results/04_filter_samples/04_filtered
mkdir
results/05_assignment/01_runs results/05_assignment/02_dereplicated results/05_assignment/03_assigned results/05_assignment/04_formated
echo
"done"
else
echo
-n
"You must set an action to perform:
\n
bash clean.sh clear "
else
echo
"Cleaning is impossible... you are not in the right folder."
fi
\ No newline at end of file
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