diff --git a/workflow/rules/3.0_genotype_likelihoods.smk b/workflow/rules/3.0_genotype_likelihoods.smk index e6b78ad..3041608 100644 --- a/workflow/rules/3.0_genotype_likelihoods.smk +++ b/workflow/rules/3.0_genotype_likelihoods.smk @@ -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} """