Commit 74a2ee39 authored by peguerin's avatar peguerin
Browse files

update relative path

parent 76036434
......@@ -4,13 +4,13 @@ __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=",")
projetMarkerRuns = dfMulti[['projmarkrun','marker','projet']].drop_duplicates()
dfpmr = projetMarkerRuns
for pmr in projetMarkerRuns.projmarkrun:
file_sample = "01_runs/"+pmr+".fasta"
file_sample = "../results/05_assignment/01_runs/"+pmr+".fasta"
if not os.path.exists(file_sample):
print("WARNING: ", file_sample," not found. We removed it from this analysis.")
dfpmr = dfpmr[dfpmr.projmarkrun != projmarkrun]
......@@ -20,21 +20,28 @@ dfpmr['fasta'] = dfpmr['marker'].map(config["assign_taxon"]["fasta"])
print(dfpmr)
###############################################################################
# RULES
###############################################################################
rule all:
input:
expand('01_runs/{run}.fasta',run=dfpmr['projmarkrun']),
expand('02_dereplicated/{run}.uniq.fasta', run=dfpmr['projmarkrun']),
expand('03_assigned/{run}.tag.u.fasta', run=dfpmr['projmarkrun']),
expand('04_formated/{run}.a.t.u.fasta', run=dfpmr['projmarkrun']),
expand('04_formated/{run}.s.a.t.u.fasta', run=dfpmr['projmarkrun']),
expand('../06_final_tables/{run}.csv', run=dfpmr['projmarkrun']),
expand('../99_log/05_assignment/02_dereplicated/{run}.log', run=dfpmr['projmarkrun']),
expand('../99_log/05_assignment/03_assign_taxon/{run}.log', run=dfpmr['projmarkrun']),
expand('../99_log/05_assignment/04_rm_attributes/{run}.log', run=dfpmr['projmarkrun']),
expand('../99_log/05_assignment/05_sort_runs/{run}.log', run=dfpmr['projmarkrun']),
expand('../99_log/05_assignment/06_table_runs/{run}.log', run=dfpmr['projmarkrun'])
include: "../00_rules/dereplicate_runs.smk"
include: "../00_rules/assign_taxon.smk"
include: "../00_rules/format_fas2tab.smk"
expand('../results/05_assignment/01_runs/{run}.fasta',run=dfpmr['projmarkrun']),
expand('../results/05_assignment/02_dereplicated/{run}.uniq.fasta', run=dfpmr['projmarkrun']),
expand('../results/05_assignment/03_assigned/{run}.tag.u.fasta', run=dfpmr['projmarkrun']),
expand('../results/05_assignment/04_formated/{run}.a.t.u.fasta', run=dfpmr['projmarkrun']),
expand('../results/05_assignment/04_formated/{run}.s.a.t.u.fasta', run=dfpmr['projmarkrun']),
expand('../results/06_final_tables/{run}.csv', run=dfpmr['projmarkrun']),
expand('../logs/05_assignment/02_dereplicated/{run}.log', run=dfpmr['projmarkrun']),
expand('../logs/05_assignment/03_assign_taxon/{run}.log', run=dfpmr['projmarkrun']),
expand('../logs/05_assignment/04_rm_attributes/{run}.log', run=dfpmr['projmarkrun']),
expand('../logs/05_assignment/05_sort_runs/{run}.log', run=dfpmr['projmarkrun']),
expand('../logs/05_assignment/06_table_runs/{run}.log', run=dfpmr['projmarkrun'])
include: "rules/dereplicate_runs.smk"
include: "rules/assign_taxon.smk"
include: "rules/rm_attributes.smk"
include: "rules/sort_runs.smk"
include: "rules/table_runs.smk"
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