Commit 4b988e06 authored by mmassaviol's avatar mmassaviol
Browse files

Debug multiple mito circos generation

parent b66226e9
......@@ -3,8 +3,6 @@ import re
import snakemake.utils
import csv
dir_path = "/workflow"
#############
# Wildcards #
#############
......@@ -308,6 +306,8 @@ rule mitoz_annotate_SE:
"then \n"
" for mito in $(grep \"mt[0-9]\{{1,\}}\" circos.dep | cut -f 1 | uniq) \n"
" do \n"
" cd {params.circos_dir} && "
" echo \"Treating mito $mito\" && "
" sed \"s/circos/circos$mito/g\" circos.conf > circos$mito.conf && "
" grep $mito circos.depth.txt > circos$mito.depth.txt && "
" grep $mito circos.karyotype.txt > circos$mito.karyotype.txt && "
......@@ -355,6 +355,8 @@ rule mitoz_annotate_PE:
"then \n"
" for mito in $(grep \"mt[0-9]\{{1,\}}\" circos.dep | cut -f 1 | uniq) \n"
" do \n"
" cd {params.circos_dir} && "
" echo \"Treating mito $mito\" && "
" sed \"s/circos/circos$mito/g\" circos.conf > circos$mito.conf && "
" grep $mito circos.depth.txt > circos$mito.depth.txt && "
" grep $mito circos.karyotype.txt > circos$mito.karyotype.txt && "
......
......@@ -35,8 +35,8 @@ def main():
if len(sys.argv) == 3:
print(sample_list(sys.argv[1],sys.argv[2]))
else:
exit("""Need two parameters: workflow name, output dir, (local_config)
Usage: ./generate_workflow.py workflow_name output_dir (local_config)""")
exit("""Needs 2 arguments: reads_directory, SeOrPe
Usage: ./get_samples.py reads_directory SeOrPe""")
if __name__ == "__main__":
# execute only if run as a script
......
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