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Expand file tree Collapse file tree Original file line number Diff line number Diff line change @@ -2,4 +2,4 @@ channels:
22 - conda-forge
33 - bioconda
44dependencies :
5- - chromsize=0.0.2
5+ - chromsize=0.0.3
Original file line number Diff line number Diff line change @@ -42,7 +42,6 @@ rule chromsize:
4242 reference_file ,
4343 output :
4444 chrom_size = cohortdir ("chrom.size" ),
45- tmp = temp_with_prefix (cohortdir ("chrom.size.tmp" )),
4645 params :
4746 CHROMSIZE = config .applications ["chromsize" ],
4847 log :
@@ -59,10 +58,8 @@ rule chromsize:
5958 threads : 1
6059 shell :
6160 r"""
62- {params.CHROMSIZE} --fasta "{input}" --output "{output.tmp}" \
63- > "{log.outfile}" 2> >(tee "{log.errfile}" >&2)
64- sed -E 's@^([^ \t]+)[^\t]*@\1@g' "{output.tmp}" > "{output.chrom_size}" \
65- 2> >(tee -a "{log.errfile}" >&2)
61+ {params.CHROMSIZE} --accession-only --fasta "{input}" --output "{output.chrom_size}" \
62+ > {log.outfile} 2> >(tee -a "{log.errfile}" >&2)
6663 """
6764
6865
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