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ONT_pilot_gitlab
Commits
9b637e54
Commit
9b637e54
authored
Mar 08, 2021
by
Valentina Galata
Browse files
preprocessing: changed qin/qout params in rm_host_bbmap_lr_metag (issue
#124
)
parent
80dc8d9c
Changes
1
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workflow/rules/preprocessing.smk
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9b637e54
...
...
@@ -162,12 +162,10 @@ rule rm_host_bbmap_lr_metag:
message:
"Preprocessing metaG long reads: bbmap - rm host contamination"
shell:
# NOTE: ignorebadquality: otherwise aborted
# qin=64: no Sanger encoding
"(date && "
"refs=$(echo \"{input.refs}\" | tr ' ' ',') && "
"bbduk.sh in={input.lr} out={output.lr} ref=\"${{refs}}\" refstats={output.stats} "
"
ignorebadquality
qin=
64
qout=
64
k=31 rcomp=t ziplevel=9 ordered=t threads={threads} && "
"qin=
33
qout=
33
k=31 rcomp=t ziplevel=9 ordered=t threads={threads} && "
# qin/qout: issue 124
"date) &> {log}"
##################################################
...
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