Commit 9b637e54 authored by Valentina Galata's avatar Valentina Galata
Browse files

preprocessing: changed qin/qout params in rm_host_bbmap_lr_metag (issue #124)

parent 80dc8d9c
...@@ -162,12 +162,10 @@ rule rm_host_bbmap_lr_metag: ...@@ -162,12 +162,10 @@ rule rm_host_bbmap_lr_metag:
message: message:
"Preprocessing metaG long reads: bbmap - rm host contamination" "Preprocessing metaG long reads: bbmap - rm host contamination"
shell: shell:
# NOTE: ignorebadquality: otherwise aborted
# qin=64: no Sanger encoding
"(date && " "(date && "
"refs=$(echo \"{input.refs}\" | tr ' ' ',') && " "refs=$(echo \"{input.refs}\" | tr ' ' ',') && "
"bbduk.sh in={input.lr} out={output.lr} ref=\"${{refs}}\" refstats={output.stats} " "bbduk.sh in={input.lr} out={output.lr} ref=\"${{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}" "date) &> {log}"
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