gffread: simplify extract cds process

src/nf_modules/gffread/main.nf

@@ -54,16 +54,7 @@ process spliced_cds {
     file_prefix = file_id
   }
   """
-gffread -x -M - -g ${fasta} ${gtf} | \
-bioawk -c fastx '{ print \$name, \$seq }' | \
-while read line; \
-do \
-name=\$(echo \$line | cut -f 1); \
-echo \$line | cut -f 2 | \
-awk -F "" '{ for (i = 3; i <= NF; i += 3) \
-printf "%s%s", \$i, (i+3>NF?"\n":FS) }' | \
-awk -v name="\$name" '{ print ">"name; print \$1 }'; \
-done \
-> ${file_prefix}.fasta
+gffread -x -M - -g ${fasta} ${gtf} \
+  > ${file_prefix}.fasta
   """
 }
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