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Fix: Make it so that bamlist generation is re-run if sample order changes, keeping meta-data consistent #51

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Sep 30, 2024
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Fix: Make it so that bamlist generation is re-run if sample order changes, keeping meta-data consistent #51

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8 changes: 6 additions & 2 deletions workflow/rules/3.0_genotype_likelihoods.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,14 @@ rule angsd_makeBamlist:
"logs/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.log",
container:
shell_container
params:
sampord=lambda w, input: f"{input.bams}",
shell:
"""
(readlink -f {input.bams} > {output}
truncate -s -1 {output}) 2> {log}
(
echo "BAM order: {params.sampord}" > {log}
readlink -f {input.bams} > {output} 2>> {log}
truncate -s -1 {output}) 2>> {log}
"""


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