Commit 24c3ad80 authored by peguerin's avatar peguerin
Browse files

add conda opt

parent 3be67b57
......@@ -11,6 +11,8 @@ rule illuminapairedend:
fq='01-illuminapairedend/{run}.fastq'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
log:
'../99-log/01-assembly/01-illuminapairedend/{run}.log'
params:
......@@ -26,6 +28,8 @@ rule remove_unaligned:
ali='02-remove_unaligned/{run}.ali.fastq'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
log:
'../99-log/01-assembly/02-remove_unaligned/{run}.log'
shell:
......
......@@ -6,6 +6,8 @@ rule assign_taxon:
'03-assigned/{run}_run.tag.u.fasta'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
params:
bdr=config["assign_taxon"]["bdr"],
fasta=config["assign_taxon"]["fasta"]
......
......@@ -7,6 +7,8 @@ rule assign_sequences:
unid='03-assign_sequences/{run}.unidentified.fastq'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
params:
barcodeFile=lambda wcs: config["barcodeFiles"][wcs.run],
barcodeFolder=config['fastqFolderPath']
......
......@@ -6,6 +6,8 @@ rule dereplicate_runs:
'02-dereplicated/{run}_run.uniq.fasta'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
log:
'../99-log/09-dereplicate_runs/{run}.log'
shell:
......
......@@ -54,6 +54,8 @@ rule rm_internal_samples:
dir='03-cleaned/{run}/'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
log:
'../99-log/08-rm_internal_samples/{run}/{sample}.log'
shell:
......
......@@ -6,6 +6,8 @@ rule rm_attributes:
'04-formated/{run}_run.a.t.u.fasta'
singularity:
config["container"]
conda:
'../96-envs/obitools_env.yaml'
log:
'../99-log/11-rm_attributes/{run}.log'
shell:
......
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