Commit 4637e3ab authored by khalid's avatar khalid
Browse files

Show mismach in blastn results

parent d3b34b20
......@@ -11,7 +11,7 @@ def <step_name>__db():
file = <step_name>__blastn_inputs()["blastdb"][0]
db_name = os.path.splitext(os.path.basename(file))[0]
db_path = os.path.dirname(file)
return { "db_name": db_name, "db_path": db_path }
rule <step_name>__blastn:
......@@ -34,7 +34,7 @@ rule <step_name>__blastn:
config["results_dir"]+'/logs/' + config["<step_name>__blastn_output_dir"] + '/blastn_log.txt'
shell:
# output header
"echo -e 'qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore\tqlen' > {output.blastout}; "
"echo -e 'qseqid\tsseqid\tpident\tlength\tmismach\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore\tqlen' > {output.blastout}; "
# command
"{params.command} "
"-query {input.query} "
......
......@@ -122,7 +122,7 @@ rule multiqc:
"-f {params.output_dir} " +
modules_to_run +
"|& tee {log};"
" sed -i 's/<meta charset="utf-8">/<meta charset="utf-8">\n<meta http-equiv="refresh" content="3000">/' {params.output_dir}/multiqc_report.html"
" sed -i 's/<meta charset=\"utf-8\">/<meta charset=\"utf-8\">\n<meta http-equiv=\"refresh\" content=\"3000\">/' {params.output_dir}/multiqc_report.html"
)
# Final Snakemake rule waiting for outputs of the final step choosen by user (default all steps)
......
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