debug cat

00-rules/cat_samples.smk

@@ -4,9 +4,6 @@ rule cat_samples:
         '03-cleaned/{run}/{sample}.c.r.l.u.fasta'
     params:
         dir='03-cleaned/{run}/'
-    output:
-        '../03-filtered/{run}.fasta'
-    log:
-        '../99-log/09-cat_samples/{run}/{sample}.log'
+        merged='../03-filtered/{run}.fasta'
     shell:
-         '''ls {input} > {log}; cat {params.dir}*.c.r.l.u.fasta > {output}'''
\ No newline at end of file
+         '''ls {input} > {log}; cat {params.dir}*.c.r.l.u.fasta > {params.merged}'''
\ No newline at end of file

02-demultiplex/Snakefile

@@ -15,8 +15,7 @@ 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/09-cat_samples/{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"