Commit 2d087661 authored by peguerin's avatar peguerin
Browse files

add singularity

parent e505a0e5
...@@ -4,6 +4,8 @@ rule dereplicate_samples: ...@@ -4,6 +4,8 @@ rule dereplicate_samples:
'01-raw/{sample}.fasta' '01-raw/{sample}.fasta'
output: output:
'02-filtered/{sample}.uniq.fasta' '02-filtered/{sample}.uniq.fasta'
singularity:
config["container"]
log: log:
'../99-log/05-dereplicate_samples/{sample}.log' '../99-log/05-dereplicate_samples/{sample}.log'
shell: shell:
...@@ -15,6 +17,8 @@ rule goodlength_samples: ...@@ -15,6 +17,8 @@ rule goodlength_samples:
'02-filtered/{sample}.uniq.fasta' '02-filtered/{sample}.uniq.fasta'
output: output:
'02-filtered/{sample}.l.u.fasta' '02-filtered/{sample}.l.u.fasta'
singularity:
config["container"]
log: log:
'../99-log/06-goodlength_samples/{sample}.log' '../99-log/06-goodlength_samples/{sample}.log'
params: params:
...@@ -29,6 +33,8 @@ rule clean_pcrerr_samples: ...@@ -29,6 +33,8 @@ rule clean_pcrerr_samples:
'02-filtered/{sample}.l.u.fasta' '02-filtered/{sample}.l.u.fasta'
output: output:
'02-filtered/{sample}.r.l.u.fasta' '02-filtered/{sample}.r.l.u.fasta'
singularity:
config["container"]
log: log:
'../99-log/07-clean_pcrerr/{sample}.log' '../99-log/07-clean_pcrerr/{sample}.log'
params: params:
...@@ -42,6 +48,8 @@ rule rm_internal_samples: ...@@ -42,6 +48,8 @@ rule rm_internal_samples:
'02-filtered/{sample}.r.l.u.fasta' '02-filtered/{sample}.r.l.u.fasta'
output: output:
'03-cleaned/{sample}.c.r.l.u.fasta' '03-cleaned/{sample}.c.r.l.u.fasta'
singularity:
config["container"]
log: log:
'../99-log/08-rm_internal_samples/{sample}.log' '../99-log/08-rm_internal_samples/{sample}.log'
shell: shell:
......
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