cat

02-demultiplex/Snakefile

@@ -3,6 +3,7 @@ __license__ = "MIT"
 
 configfile: "../config.yaml"
 
+RUNS, = glob_wildcards('raw/{run}_R1.fastq.gz')
 
 SAMPLES, = glob_wildcards('01-raw/{sample}.fasta')
 
@@ -11,7 +12,8 @@ rule all:
         expand('02-filtered/{sample}.uniq.fasta',sample=SAMPLES),
         expand('02-filtered/{sample}.l.u.fasta',sample=SAMPLES),
         expand('02-filtered/{sample}.r.l.u.fasta',sample=SAMPLES),
-        expand('03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES),        
+        expand('03-cleaned/{sample}.c.r.l.u.fasta',sample=SAMPLES),
+        expand('03-cleaned/{run}_{sa}.c.r.l.u.fasta',run=RUNS),     
         expand('../99-log/05-dereplicate_samples/{sample}.log',sample=SAMPLES),
         expand('../99-log/06-goodlength_samples/{sample}.log',sample=SAMPLES),
         expand('../99-log/07-clean_pcrerr/{sample}.log',sample=SAMPLES),
@@ -19,3 +21,12 @@ rule all:
 
 include: "../00-rules/filtered.smk"
 
+
+### Concatenate sequences from each sample of the same run
+rule cat_samples:
+    input:
+        '03-cleaned/{run}_{sa}.c.r.l.u.fasta'
+    output:
+         '03-filtered/{run}_run.fasta'
+    shell:
+         '''cat {input} > {output}'''
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