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[version bump] chromsize now cleans headers
- no more need for awk scriplet
1 parent 5e7bf8b commit 0b6841f

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Lines changed: 3 additions & 6 deletions

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workflow/envs/chromsize.yaml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,4 +2,4 @@ channels:
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- conda-forge
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- bioconda
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dependencies:
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- chromsize=0.0.2
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- chromsize=0.0.3

workflow/rules/mafs.smk

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@@ -42,7 +42,6 @@ rule chromsize:
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reference_file,
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output:
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chrom_size=cohortdir("chrom.size"),
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tmp=temp_with_prefix(cohortdir("chrom.size.tmp")),
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params:
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CHROMSIZE=config.applications["chromsize"],
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log:
@@ -59,10 +58,8 @@ rule chromsize:
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threads: 1
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shell:
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r"""
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{params.CHROMSIZE} --fasta "{input}" --output "{output.tmp}" \
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> "{log.outfile}" 2> >(tee "{log.errfile}" >&2)
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sed -E 's@^([^ \t]+)[^\t]*@\1@g' "{output.tmp}" > "{output.chrom_size}" \
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2> >(tee -a "{log.errfile}" >&2)
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{params.CHROMSIZE} --accession-only --fasta "{input}" --output "{output.chrom_size}" \
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> {log.outfile} 2> >(tee -a "{log.errfile}" >&2)
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"""
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