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Laura Denies
PathoFact
Commits
c0f66042
Commit
c0f66042
authored
Jun 18, 2020
by
Laura Denies
Browse files
adjusted ORFs ID translation
parent
01b6b60d
Changes
2
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rules/AMR/Combine_MGE_AMR.smk
View file @
c0f66042
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@@ -11,7 +11,7 @@ rule combine_AMR_plasmid:
input:
AMR="{datadir}/{project}/AMR/deepARG_results/{sample}.out.mapping.ARG",
AMR_translation="{datadir}/{project}/renamed/{sample}_translation.tsv",
Plasmid="{datadir}/{project}/MGE/PlasFlow
/plasmid
/{sample}_plasflow_prediction_final.tsv",
Plasmid="{datadir}/{project}/MGE/
plasmid/
PlasFlow/{sample}_plasflow_prediction_final.tsv",
Contig_translation="{datadir}/{project}/renamed/{sample}_Contig_translation.tsv",
Contig_gene_list="{datadir}/{project}/Prodigal/{sample}.contig",
VirFinder="{datadir}/{project}/MGE/phage/{sample}_VirFinder_aggregated.csv",
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rules/Universal/Preprocessing.smk
View file @
c0f66042
...
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@@ -66,7 +66,7 @@ rule generate_ID:
rule generate_translation:
input:
renamed="{datadir}/{project}/renamed/{sample}_ID.faa",
original="{datadir}/{sample}.faa"
original="{datadir}/{
project}/Prodigal/{
sample}.faa"
output:
"{datadir}/{project}/renamed/{sample}_translation.tsv"
message:
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