add conda env

03_demultiplex/rules/assign_sequences.smk

@@ -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:        

03_demultiplex/rules/split_sequences.smk

@@ -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:

04_filter_samples/rules/clean_pcrerr_samples.smk

@@ -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:

04_filter_samples/rules/dereplicate_samples.smk

@@ -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:

04_filter_samples/rules/goodlength_samples.smk

@@ -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:

04_filter_samples/rules/rm_internal_samples.smk

@@ -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:

05_assignment/rules/assign_taxon.smk

@@ -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:

05_assignment/rules/dereplicate_runs.smk

@@ -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:

05_assignment/rules/rm_attributes.smk

@@ -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:

05_assignment/rules/sort_runs.smk

@@ -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:

05_assignment/rules/table_runs.smk

@@ -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: