diff --git a/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.rule.snakefile b/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.rule.snakefile index 850f6df149da4f5b45803389f9fae99e181f1b31..b80e7772dbe83a7684cf8b5f609b20ed6db4bb6a 100755 --- a/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.rule.snakefile +++ b/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.rule.snakefile @@ -15,9 +15,7 @@ rule <step_name>__mitoz_findmitoscaf: # Si l'on veut eviter l'étape cal_bwa_abundance.py qui fait un mapping couteux sur tous les scaffolds de l'assemblage : # convert Megahit or flye output to format similar to one produced by abundance estimate procedure with a dummy abundance of 0.1 # N.B. assembly fasta file must be one line per sequence format - """awk '{{posit = index($0,">"); if (posit == 1) {{split($0,a," "); sub(">",">C",a[1]); ident=a[1]"\\t100.0\\tlength="}} else {{long=length($0);if (long > 0) {{ident=ident long; print ident"\\n"$0 }} }}}}' {input.fasta} > /tmp/assembly.contigs.fa;""" - "mkdir -p {params.output_dir} && " "cd {params.output_dir}; " "{params.command} "