Commit 8ff01002 authored by peguerin's avatar peguerin
Browse files

define new rules

parent d418dd03
......@@ -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"
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