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edna
snakemake_only_obitools
Commits
2d087661
Commit
2d087661
authored
Nov 14, 2019
by
peguerin
Browse files
add singularity
parent
e505a0e5
Changes
1
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00-rules/filtered.smk
View file @
2d087661
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@@ -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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