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add deduplication of sequences by ID in augur_from_assemblies #564

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merged 3 commits into from
Nov 5, 2024
Merged

add deduplication of sequences by ID in augur_from_assemblies #564

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ed410a8
add deduplication of sequences by ID in augur_from_assemblies
tomkinsc Oct 28, 2024
da997e1
Merge branch 'master' into ct-dedup-sequences-in-augur_from_assemblies
tomkinsc Nov 5, 2024
eaeee77
Merge branch 'master' into ct-dedup-sequences-in-augur_from_assemblies
tomkinsc Nov 5, 2024
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6 changes: 5 additions & 1 deletion pipes/WDL/workflows/augur_from_assemblies.wdl
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Expand Up @@ -67,9 +67,13 @@ workflow augur_from_assemblies {
sequences_fasta = zcat.combined,
min_non_N = min_unambig_genome
}
call nextstrain.nextstrain_deduplicate_sequences as dedup_seqs {
input:
sequences_fasta = filter_sequences_by_length.filtered_fasta
}
call nextstrain.mafft_one_chr as mafft {
input:
sequences = filter_sequences_by_length.filtered_fasta,
sequences = dedup_seqs.sequences_deduplicated_fasta,
ref_fasta = ref_fasta,
basename = "all_samples_aligned.fasta"
}
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