Commit d5760922 authored by peguerin's avatar peguerin
Browse files

add conda env

parent 21783deb
......@@ -3,6 +3,8 @@ rule assign_sequences:
output:
assign='../results/03_demultiplex/01_assign_sequences/{demultiplex}.ali.assigned.fastq',
unid='../results/03_demultiplex/01_assign_sequences/{demultiplex}.unidentified.fastq'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
params:
......
......@@ -4,6 +4,8 @@ rule split_sequences:
'../results/03_demultiplex/01_assign_sequences/{demultiplex}.ali.assigned.fastq'
params:
dir='../results/03_demultiplex/02_raw/{demultiplex}/'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule clean_pcrerr_samples:
'../results/04_filter_samples/02_goodlength/{demultiplexs}.l.u.fasta'
output:
'../results/04_filter_samples/03_clean_pcrerr/{demultiplexs}.r.l.u.fasta'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule dereplicate_samples:
'../results/03_demultiplex/02_raw/{demultiplexs}.fasta'
output:
'../results/04_filter_samples/01_dereplicated/{demultiplexs}.uniq.fasta'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule goodlength_samples:
'../results/04_filter_samples/01_dereplicated/{demultiplexs}.uniq.fasta'
output:
'../results/04_filter_samples/02_goodlength/{demultiplexs}.l.u.fasta'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule rm_internal_samples:
'../results/04_filter_samples/03_clean_pcrerr/{demultiplexs}.r.l.u.fasta'
output:
'../results/04_filter_samples/04_filtered/{demultiplexs}.c.r.l.u.fasta'
conda:
'../envs/obitools_envs.yaml'
params:
dmulti= lambda wildcards: dfMultiChecked[dfMultiChecked.demultiplex == wildcards.demultiplexs].to_dict('records')[0],
singularity:
......
......@@ -6,6 +6,8 @@ rule assign_taxon:
'../results/05_assignment/03_assigned/{run}.tag.u.fasta'
threads:
workflow.cores * 0.5
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
params:
......
......@@ -4,6 +4,8 @@ rule dereplicate_runs:
'../results/05_assignment/01_runs/{run}.fasta'
output:
'../results/05_assignment/02_dereplicated/{run}.uniq.fasta'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule rm_attributes:
'../results/05_assignment/03_assigned/{run}.tag.u.fasta'
output:
'../results/05_assignment/04_formated/{run}.a.t.u.fasta'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule sort_runs:
'../results/05_assignment/04_formated/{run}.a.t.u.fasta'
output:
'../results/05_assignment/04_formated/{run}.s.a.t.u.fasta'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
log:
......
......@@ -4,6 +4,8 @@ rule table_runs:
'../results/05_assignment/04_formated/{run}.s.a.t.u.fasta'
output:
'../results/06_final_tables/{run}.csv'
conda:
'../envs/obitools_envs.yaml'
singularity:
config["singularity"]["obitools"]
params:
......
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