Commit 01a9ebc5 authored by peguerin's avatar peguerin
Browse files

conda env add to rules

parent 848d9dcb
...@@ -26,6 +26,8 @@ rule split_sequences: ...@@ -26,6 +26,8 @@ rule split_sequences:
dir='../02-demultiplex/01-raw/{run}/' dir='../02-demultiplex/01-raw/{run}/'
singularity: singularity:
config["container"] config["container"]
conda:
'../96-envs/obitools_env.yaml'
log: log:
'../99-log/01-assembly/04-split_sequences/{run}.log' '../99-log/01-assembly/04-split_sequences/{run}.log'
shell: shell:
......
...@@ -6,6 +6,8 @@ rule dereplicate_samples: ...@@ -6,6 +6,8 @@ rule dereplicate_samples:
'02-filtered/{run}/{sample}.uniq.fasta' '02-filtered/{run}/{sample}.uniq.fasta'
singularity: singularity:
config["container"] config["container"]
conda:
'../96-envs/obitools_env.yaml'
log: log:
'../99-log/05-dereplicate_samples/{run}/{sample}.log' '../99-log/05-dereplicate_samples/{run}/{sample}.log'
params: params:
...@@ -21,6 +23,8 @@ rule goodlength_samples: ...@@ -21,6 +23,8 @@ rule goodlength_samples:
'02-filtered/{run}/{sample}.l.u.fasta' '02-filtered/{run}/{sample}.l.u.fasta'
singularity: singularity:
config["container"] config["container"]
conda:
'../96-envs/obitools_env.yaml'
log: log:
'../99-log/06-goodlength_samples/{run}/{sample}.log' '../99-log/06-goodlength_samples/{run}/{sample}.log'
params: params:
...@@ -37,6 +41,8 @@ rule clean_pcrerr_samples: ...@@ -37,6 +41,8 @@ rule clean_pcrerr_samples:
'02-filtered/{run}/{sample}.r.l.u.fasta' '02-filtered/{run}/{sample}.r.l.u.fasta'
singularity: singularity:
config["container"] config["container"]
conda:
'../96-envs/obitools_env.yaml'
log: log:
'../99-log/07-clean_pcrerr/{run}/{sample}.log' '../99-log/07-clean_pcrerr/{run}/{sample}.log'
params: params:
......
...@@ -29,6 +29,8 @@ rule sort_runs: ...@@ -29,6 +29,8 @@ rule sort_runs:
'04-formated/{run}_run.s.a.t.u.fasta' '04-formated/{run}_run.s.a.t.u.fasta'
singularity: singularity:
config["container"] config["container"]
conda:
'../96-envs/obitools_env.yaml'
log: log:
'../99-log/12-sort_runs/{run}.log' '../99-log/12-sort_runs/{run}.log'
shell: shell:
...@@ -42,6 +44,8 @@ rule table_runs: ...@@ -42,6 +44,8 @@ rule table_runs:
'../04-final_tables/{run}.csv' '../04-final_tables/{run}.csv'
singularity: singularity:
config["container"] config["container"]
conda:
'../96-envs/obitools_env.yaml'
log: log:
'../99-log/13-table_runs/{run}.log' '../99-log/13-table_runs/{run}.log'
shell: shell:
......
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