individual rules for step 03

03_demultiplex/rules/assign_sequences.smk

+### Assign each sequence record to the corresponding sample/marker combination
+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'
+    singularity:
+        config["singularity"]["obitools"]
+    params:        
+        dmulti= lambda wildcards: dfRunMarker[dfRunMarker.projMarkRun == wildcards.demultiplex].to_dict('records')[0],
+    log:
+        '../logs/03_demultiplex/01_assign_sequences/{demultiplex}.log'
+    shell:
+        '''ngsfilter -t {params.dmulti[dat]} -u {output.unid} ../02_assembly/02_remove_unaligned/{params.dmulti[run]}.ali.fastq --fasta-output > {output.assign} 2> {log}'''
+

03_demultiplex/rules/split_sequences.smk

+### Split the input sequence file in a set of subfiles according to the values of attribute `sample`
+rule split_sequences:
+    input:
+        '../results/03_demultiplex/01_assign_sequences/{demultiplex}.ali.assigned.fastq'
+    params:
+        dir='../results/03_demultiplex/02_raw/{demultiplex}/'
+    singularity:
+        config["singularity"]["obitools"]
+    log:
+        '../logs/03_demultiplex/02_split_sequences/{demultiplex}.log'
+    shell:
+        '''mkdir -p {params.dir}; obisplit -p "{params.dir}" -t sample --fasta {input} 2> {log}'''