add containers to all rules

ktmeaton · Oct 9, 2020 · efd256e · efd256e
1 parent 636db83
commit efd256e
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Showing 4 changed files with 24 additions and 0 deletions.
diff --git a/workflow/rules/alignment.smk b/workflow/rules/alignment.smk
@@ -25,6 +25,8 @@ rule eager:
         reads_origin = "(sra|local)",
     conda:
         os.path.join(envs_dir,"eager","eager.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:eager"
     log:
         html = os.path.join(logs_dir, "eager", "{reads_origin}", "{sample}.html"),
         txt = os.path.join(logs_dir, "eager", "{reads_origin}", "{sample}.log"),
@@ -75,6 +77,8 @@ rule snippy_pairwise:
         reads_origin="(sra|local|assembly)",
     conda:
         os.path.join(envs_dir,"align","align.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:align"
     shell:
         "if [[ {wildcards.reads_origin} == 'assembly' ]]; then \
             snippy \
@@ -135,6 +139,8 @@ rule snippy_multi:
         os.path.join(logs_dir, "snippy_multi","snippy-core.log")
     conda:
         os.path.join(envs_dir,"align","align.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:align"
     resources:
         cpus = 1,
     shell:

diff --git a/workflow/rules/filter_mask.smk b/workflow/rules/filter_mask.smk
@@ -18,6 +18,8 @@ rule detect_repeats:
         logs_dir + "/detect_repeats/{reads_origin}/{sample}.log",
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     resources:
         cpus = 1,
     shell:
@@ -41,6 +43,8 @@ rule detect_low_complexity:
         reads_origin = "(reference|assembly)",
     conda:
         os.path.join(envs_dir,"eager","eager.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:eager"
     resources:
         cpus = 1,
     shell:
@@ -61,6 +65,8 @@ rule detect_snp_density:
         reads_origin = "(assembly|sra|local)",
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     log:
       os.path.join(logs_dir, "detect_snp_density","{reads_origin}","{sample}.log"),
     resources:
@@ -88,6 +94,8 @@ rule merge_snp_density:
               density=config["snippy_snp_density"])
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     resources:
         cpus = 1,
     shell:
@@ -107,6 +115,8 @@ rule snippy_multi_extract:
                       locus_name=config["reference_locus_name"]),
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     resources:
         cpus = 1,
     shell:
@@ -137,6 +147,8 @@ rule snippy_multi_filter:
         missing = float(config["snippy_missing_data"] / 100)
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     resources:
         cpus = 1,
     shell:

diff --git a/workflow/rules/phylogeny.smk b/workflow/rules/phylogeny.smk
@@ -29,6 +29,8 @@ rule iqtree:
         seed = config["iqtree_seed"]
     conda:
         os.path.join(envs_dir,"phylogeny","phylogeny.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:phylogeny"
     log:
         os.path.join(logs_dir, "iqtree","iqtree.core-filter" + str(config["snippy_missing_data"]) + ".log")
     shell:

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -14,6 +14,8 @@ rule qualimap:
         html = results_dir + "/qualimap/{reads_origin}/{sample}/qualimapReport.html",
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     log:
         os.path.join(logs_dir, "qualimap", "{reads_origin}", "{sample}.log")
     shell:
@@ -61,6 +63,8 @@ rule multiqc:
         dir = directory(results_dir + "/multiqc/"),
     conda:
         os.path.join(envs_dir,"qc","qc.yaml")
+    container:
+        "docker://ktmeaton/plague-phylogeography:qc"
     log:
         os.path.join(logs_dir, "multiqc/multiqc.log")
     resources: