params coma

00-rules/cat_samples.smk

@@ -5,5 +5,7 @@ rule cat_samples:
     params:
         dir='03-cleaned/{run}/',
         merged='../03-filtered/{run}.fasta'
+    log:
+        '../99-log/09-cat_samples/{run}/{sample}.log'
     shell:
          '''ls {input} > {log}; cat {params.dir}*.c.r.l.u.fasta > {params.merged}'''
\ No newline at end of file

02-demultiplex/Snakefile

@@ -15,7 +15,8 @@ rule all:
         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)
+        expand('../99-log/08-rm_internal_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES),
+        expand('../99-log/09-cat_samples/{run}/{sample}.log',zip, run=RUNS, sample=SAMPLES)
 
 include: "../00-rules/filter_samples.smk"
 include: "../00-rules/cat_samples.smk"