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Tcoffee tcs #5288

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merged 11 commits into from
Mar 20, 2024
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fixing trailing whitespaces
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alessiovignoli committed Mar 20, 2024
commit b0f0681f4489586940e53a2aa242408ebc73b4a9
6 changes: 3 additions & 3 deletions modules/nf-core/tcoffee/tcs/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -26,14 +26,14 @@ process TCOFFEE_TCS {
def header = meta.keySet().join(",")
def values = meta.values().join(",")
def unzipped_name = msa.toString() - '.gz'
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Align equal signs

"""
"""
export TEMP='./'
filename=${msa}
if [[ \$(basename $msa) == *.gz ]] ; then
unpigz -f $msa
filename=${unzipped_name}
fi

# Bad hack to circumvent t_coffee bug
# Issue described already in: https://github.com/cbcrg/tcoffee/issues/3
# Add an A in front of filename if the file begins with A
Expand All @@ -43,7 +43,7 @@ process TCOFFEE_TCS {
t_coffee -infile \$input \
-evaluate -output=score_ascii \
${lib_arg} \
-outfile ${prefix}.tcs
-outfile ${prefix}.tcs

# Add metadata info to output file
echo "${header},TCS" > "${prefix}.scores"
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2 changes: 1 addition & 1 deletion modules/nf-core/tcoffee/tcs/meta.yml
Original file line number Diff line number Diff line change
Expand Up @@ -54,4 +54,4 @@ output:
pattern: "*.scores"

authors:
- "@alessiovignoli"
- "@alessiovignoli"
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