Skip to content
Snippets Groups Projects
Commit 008f818e authored by Blaise Li's avatar Blaise Li
Browse files

Fix methods message with empty placeholder.

parent 8e48eccb
No related branches found
No related tags found
No related merge requests found
...@@ -71,7 +71,7 @@ with NamedTemporaryFile() as fastq, NamedTemporaryFile() as rates_record: ...@@ -71,7 +71,7 @@ with NamedTemporaryFile() as fastq, NamedTemporaryFile() as rates_record:
if hasattr(snakemake.output, "methods"): if hasattr(snakemake.output, "methods"):
shell(f"cp {snakemake.input.methods} {snakemake.output.methods}") shell(f"cp {snakemake.input.methods} {snakemake.output.methods}")
methods = f"# {snakemake.rule}\nThe first {} {snakemake.params.read_name} reads were mapped on the {snakemake.params.genome_name} using {snakemake.params.aligner} (version ${{{{v}}}}) with options {snakemake.params.settings}." methods = f"# {snakemake.rule}\nThe first 10000 {snakemake.params.read_name} reads were mapped on the {snakemake.params.genome_name} using {snakemake.params.aligner} (version ${{{{v}}}}) with options {snakemake.params.settings}. Among those settings, the one resulting in the highest mapping rate was retained."
shell(f""" shell(f"""
v=$({snakemake.params.aligner} --version | head -1 | awk '{{{{print $3}}}}') v=$({snakemake.params.aligner} --version | head -1 | awk '{{{{print $3}}}}')
echo "{methods}" >> {snakemake.output.methods} echo "{methods}" >> {snakemake.output.methods}
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment