rename path filter

00-rules/filtered.smk

 ### dereplicate reads into uniq sequences
 rule dereplicate_samples:
     input:
-        '02-demultiplex/02-01-raw/{sample}.fasta'
+        '01-raw/{sample}.fasta'
     output:
-        '02-demultiplex/02-02-filtered/{sample}.uniq.fasta'
+        '02-filtered/{sample}.uniq.fasta'
     log:
-        'log/dereplicate_samples/{sample}.log'
+        '../99-log/05-dereplicate_samples/{sample}.log'
     shell:
         '''obiuniq -m sample {input} > {output} 2> {log}'''
 
 ### only sequence more than 20bp with no ambiguity IUAPC with total coverage greater than 10 reads
 rule goodlength_samples:
     input:
-        '02-demultiplex/02-02-filtered/{sample}.uniq.fasta'
+        '02-filtered/{sample}.uniq.fasta'
     output:
-        '02-demultiplex/02-02-filtered/{sample}.l.u.fasta'
+        '02-filtered/{sample}.l.u.fasta'
     log:
-        'log/goodlength_samples/{sample}.log'
+        '../99-log/06-goodlength_samples/{sample}.log'
     params:
          count=config["good_length_samples"]["count"],
          seq_length=config["good_length_samples"]["seq_length"]
@@ -26,11 +26,11 @@ rule goodlength_samples:
 ### Clean the sequences for PCR/sequencing errors (sequence variants)
 rule clean_pcrerr_samples:
     input:
-        '02-demultiplex/02-02-filtered/{sample}.l.u.fasta'
+        '02-filtered/{sample}.l.u.fasta'
     output:
-        '02-demultiplex/02-02-filtered/{sample}.r.l.u.fasta'
+        '02-filtered/{sample}.r.l.u.fasta'
     log:
-        'log/clean_pcrerr/{sample}.log'
+        '../99-log/07-clean_pcrerr/{sample}.log'
     params:
          r=config["clean_pcrerr_samples"]["r"]
     shell:
@@ -39,11 +39,11 @@ rule clean_pcrerr_samples:
 ### Remove sequence which are classified as 'internal' by obiclean
 rule rm_internal_samples:
     input:
-        '02-demultiplex/02-02-filtered/{sample}.r.l.u.fasta'
+        '02-filtered/{sample}.r.l.u.fasta'
     output:
-        '02-demultiplex/02-03-cleaned/{sample}.c.r.l.u.fasta'
+        '03-cleaned/{sample}.c.r.l.u.fasta'
     log:
-        'log/rm_internal_samples/{sample}.log'
+        '../99-log/08-rm_internal_samples/{sample}.log'
     shell:
         '''obigrep -p 'obiclean_internalcount == 0' {input} > {output} 2> {log}'''
 

02-demultiplex/Snakefile

@@ -10,10 +10,10 @@ rule all:
         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('../99-log/dereplicate_samples/{sample}.log',sample=SAMPLES),
-        expand('../99-log/goodlength_samples/{sample}.log',sample=SAMPLES),
-        expand('../99-log/clean_pcrerr/{sample}.log',sample=SAMPLES),
-        expand('../99-log/rm_internal_samples/{sample}.log',sample=SAMPLES)
+        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),
+        expand('../99-log/08-rm_internal_samples/{sample}.log',sample=SAMPLES)
 
 include: "../00-rules/filtered.smk"