edit path snakefile

03_demultiplex/Snakefile

@@ -26,13 +26,10 @@ def str_join(df, sep, *cols):
 #configfile: "01_infos/config.yaml"
 
 
-dfMulti =pandas.read_csv("../01_infos/all_demultiplex.csv", sep=",")
+dfMulti =pandas.read_csv("all_demultiplex.csv", sep=",")
 
 
-
-
-
-rapidrunfile = "../"+config['fichiers']['rapidrun']
+rapidrunfile = config['fichiers']['rapidrun']
 #rapidrunfile="../01_infos/all_samples.tsv"
 
 dfr =pandas.read_csv(rapidrunfile, sep="\t")
@@ -89,13 +86,20 @@ for projmarkerrun in dfRunMarker['projMarkRun'].unique():
     else:
         print("Writing sample description files for project and marker", thisProj, thisMarker, ":", "WARNING no information about it, check the file", rapidrunfile, "or blacklist this project")
     
-dfRunMarker['dat'] = ["00_dat/"+ele.replace('/','_')+".tsv" for ele in dfRunMarker['projMarkRun']]   
+dfRunMarker['dat'] = ["../results/03_demultiplex/00_dat/"+ele.replace('/','_')+".tsv" for ele in dfRunMarker['projMarkRun']]
+
+
+###############################################################################
+# RULES
+###############################################################################
 
 rule all:
     input:
-       expand('01_assign_sequences/{demultiplex}.ali.assigned.fastq', demultiplex=dfRunMarker.projMarkRun),
-       expand('01_assign_sequences/{demultiplex}.unidentified.fastq', demultiplex=dfRunMarker.projMarkRun),
-       expand('../99_log/03_demultiplex/01_assign_sequences/{demultiplex}.log', demultiplex=dfRunMarker.projMarkRun),
-       expand('../99_log/03_demultiplex/02_split_sequences/{demultiplex}.log', demultiplex=dfRunMarker.projMarkRun)
+       expand('../results/03_demultiplex/01_assign_sequences/{demultiplex}.ali.assigned.fastq', demultiplex=dfRunMarker.projMarkRun),
+       expand('../results/03_demultiplex/01_assign_sequences/{demultiplex}.unidentified.fastq', demultiplex=dfRunMarker.projMarkRun),
+       expand('../logs/03_demultiplex/01_assign_sequences/{demultiplex}.log', demultiplex=dfRunMarker.projMarkRun),
+       expand('../logs/03_demultiplex/02_split_sequences/{demultiplex}.log', demultiplex=dfRunMarker.projMarkRun)
+
+include: "rules/assign_sequences.smk"
+include: "rules/split_sequences.smk"
 
-include: "../00_rules/demultiplex.smk"