Commit c7040b60 authored by peguerin's avatar peguerin
Browse files

edit path snakefile

parent ac98e5d3
......@@ -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"
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