Fix deeparg container version

pha4ge · Jun 29, 2020 · 8a3634b · 8a3634b
1 parent 189bae8
commit 8a3634b
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/Snakefile b/Snakefile
@@ -35,7 +35,7 @@ rule cleanup:
         expand("results/{sample}/srax/Results/sraX_analysis.html", sample=samples.index),
         expand("results/{sample}/sstar/report.tsv", sample=samples.index),
         expand("results/{sample}/kmerresistance/results.KmerRes", sample=samples.index),
-        #expand("results/{sample}/deeparg/output.mapping.ARG", sample=samples.index),
+        expand("results/{sample}/deeparg/output.mapping.ARG", sample=samples.index),
         #expand("results/{sample}/srst2/srst2__fullgenes__ResFinder__results.txt", sample=samples.index)
     output:
         "pipeline_finished.txt"
@@ -45,8 +45,8 @@ rule cleanup:
         touch pipeline_finished.txt
         """
 
-#include: "rules/deeparg.smk"
 #include: "rules/srst2.smk" 
+include: "rules/deeparg.smk"
 include: "rules/abricate.smk"
 include: "rules/amrfinder.smk"
 include: "rules/ariba.smk"

diff --git a/rules/deeparg.smk b/rules/deeparg.smk
@@ -5,7 +5,7 @@ rule run_deeparg:
         report = "results/{sample}/deeparg/output.mapping.ARG",
         report_potential = "results/{sample}/deeparg/output.mapping.potential.ARG"
     singularity:
-        "docker://gaarangoa/deeparg:latest"
+        "docker://gaarangoa/deeparg:v1.0.1"
     shell:
         """
         python /deeparg/deepARG.py --align --type nucl --reads --input /data/results/{wildcards.sample}/deeparg/reads.fasta --output /data/results/{wildcards.sample}/deeparg/output