define new rules

04_filter_samples/Snakefile

@@ -6,7 +6,7 @@ __license__ = "MIT"
 import pandas
 import os.path
 
-dfMulti = pandas.read_csv("../01_infos/all_demultiplex.csv", sep=",")
+dfMulti =pandas.read_csv("../results/01_settings/all_demultiplex.csv", sep=",")
 
 ## check demultiplexing results
 
@@ -20,15 +20,22 @@ for thisDemultiplex in dfMulti.demultiplex:
 
 print(dfMultiChecked)
 
+###############################################################################
+# RULES
+###############################################################################
+
 rule all:
     input:
-        expand('01_dereplicated/{demultiplexs}.uniq.fasta', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('02_goodlength/{demultiplexs}.l.u.fasta', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('03_clean_pcrerr/{demultiplexs}.r.l.u.fasta', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('04_filtered/{demultiplexs}.c.r.l.u.fasta', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('../99_log/04_filter_samples/01_dereplicated/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('../99_log/04_filter_samples/02_goodlength/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('../99_log/04_filter_samples/03_clean_pcrerr/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex']),
-        expand('../99_log/04_filter_samples/04_filtered/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex'])
+        expand('../results/04_filter_samples/01_dereplicated/{demultiplexs}.uniq.fasta', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../results/04_filter_samples/02_goodlength/{demultiplexs}.l.u.fasta', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../results/04_filter_samples/03_clean_pcrerr/{demultiplexs}.r.l.u.fasta', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../results/04_filter_samples/04_filtered/{demultiplexs}.c.r.l.u.fasta', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../logs/04_filter_samples/01_dereplicated/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../logs/04_filter_samples/02_goodlength/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../logs/04_filter_samples/03_clean_pcrerr/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex']),
+        expand('../logs/04_filter_samples/04_filtered/{demultiplexs}.log', demultiplexs=dfMultiChecked['demultiplex'])
         
-include: "../00_rules/filter_samples.smk"
+include: "rules/dereplicate_samples.smk"
+include: "rules/goodlength_samples.smk"
+include: "rules/clean_pcrerr_samples.smk"
+include: "rules/rm_internal_samples.smk"