adjusted ORFs ID translation

c0f66042 · Laura Denies · 01b6b60d · c0f66042 · c0f66042
Commit c0f66042 authored Jun 18, 2020 by Laura Denies
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rules/AMR/Combine_MGE_AMR.smk rules/AMR/Combine_MGE_AMR.smk +1 -1

rules/Universal/Preprocessing.smk rules/Universal/Preprocessing.smk +1 -1

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--- a/rules/AMR/Combine_MGE_AMR.smk
+++ b/rules/AMR/Combine_MGE_AMR.smk
@@ -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",

--- a/rules/Universal/Preprocessing.smk
+++ b/rules/Universal/Preprocessing.smk
@@ -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: