cat

00-rules/cat_samples.smk

+### Concatenate sequences from each sample of the same run
+rule cat_samples:
+    input:
+        '03-cleaned/{run}/{sample}.c.r.l.u.fasta'
+    params:
+        dir='03-cleaned/{run}/'
+    output:
+        '../03-filtered/{run}.fasta'
+    shell:
+         '''cat {params.dir}*.c.r.l.u.fasta > {output}'''
\ No newline at end of file

00-rules/demultiplex.smk

@@ -21,10 +21,10 @@ rule split_sequences:
     input:
         '03-assign_sequences/{run}.ali.assigned.fastq'
     params:
-        '../02-demultiplex/01-raw/{run}/'
+        dir='../02-demultiplex/01-raw/{run}/'
     singularity:
         config["container"]
     log:
         '../99-log/01-assembly/04-split_sequences/{run}.log'
     shell:
-        '''mkdir -p {params}; obisplit -p "{params}" -t sample --fasta {input} 2> {log}'''
+        '''mkdir -p {params.dir}; obisplit -p "{params}" -t sample --fasta {input} 2> {log}'''

02-demultiplex/Snakefile

@@ -12,11 +12,11 @@ rule all:
         expand('02-filtered/{run}/{sample}.l.u.fasta',zip, run=RUNS, sample=SAMPLES),
         expand('02-filtered/{run}/{sample}.r.l.u.fasta',zip, run=RUNS, sample=SAMPLES),
         expand('03-cleaned/{run}/{sample}.c.r.l.u.fasta',zip, run=RUNS, sample=SAMPLES),
-        expand('../03-filtered/{run}.fasta',run=config["fastqFiles"]),
         expand('../99-log/05-dereplicate_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
         expand('../99-log/06-goodlength_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
         expand('../99-log/07-clean_pcrerr/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
         expand('../99-log/08-rm_internal_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES)
 
 include: "../00-rules/filter_samples.smk"
+include: "../00-rules/cat_samples.smk"