add singularity

00-rules/filtered.smk

@@ -4,6 +4,8 @@ rule dereplicate_samples:
         '01-raw/{sample}.fasta'
     output:
         '02-filtered/{sample}.uniq.fasta'
+    singularity:
+        config["container"]
     log:
         '../99-log/05-dereplicate_samples/{sample}.log'
     shell:
@@ -15,6 +17,8 @@ rule goodlength_samples:
         '02-filtered/{sample}.uniq.fasta'
     output:
         '02-filtered/{sample}.l.u.fasta'
+    singularity:
+        config["container"]
     log:
         '../99-log/06-goodlength_samples/{sample}.log'
     params:
@@ -29,6 +33,8 @@ rule clean_pcrerr_samples:
         '02-filtered/{sample}.l.u.fasta'
     output:
         '02-filtered/{sample}.r.l.u.fasta'
+    singularity:
+        config["container"]
     log:
         '../99-log/07-clean_pcrerr/{sample}.log'
     params:
@@ -42,6 +48,8 @@ rule rm_internal_samples:
         '02-filtered/{sample}.r.l.u.fasta'
     output:
         '03-cleaned/{sample}.c.r.l.u.fasta'
+    singularity:
+        config["container"]
     log:
         '../99-log/08-rm_internal_samples/{sample}.log'
     shell: