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Verified Commit cd5218a0 authored by Laurent Modolo's avatar Laurent Modolo
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gffread: escape $ :61

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src/nf_modules/gffread/main.nf
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...@@ -58,7 +58,7 @@ gffread -x -M - -g ${fasta} ${gtf} | \ ...@@ -58,7 +58,7 @@ gffread -x -M - -g ${fasta} ${gtf} | \
bioawk -c fastx '{ print \$name, \$seq }' | \ bioawk -c fastx '{ print \$name, \$seq }' | \
while read line; \ while read line; \
do \ do \
name=$(echo \$line | cut -f 1); \ name=\$(echo \$line | cut -f 1); \
echo \$line | cut -f 2 | \ echo \$line | cut -f 2 | \
awk -F "" '{ for (i = 3; i <= NF; i += 3) \ awk -F "" '{ for (i = 3; i <= NF; i += 3) \
printf "%s%s", \$i, (i+3>NF?"\n":FS) }' | \ printf "%s%s", \$i, (i+3>NF?"\n":FS) }' | \
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