Log sequence sanitizer output to its own file to improve debugging
@@ -62,7 +62,8 @@ rule align:
basename = "seqs_{origin}",
strain_prefixes=config["strip_strain_prefixes"],
# Strip the compression suffix for the intermediate output from the aligner.
- uncompressed_alignment=lambda wildcards, output: Path(output.alignment).with_suffix("")
+ uncompressed_alignment=lambda wildcards, output: Path(output.alignment).with_suffix(""),
+ sanitize_log="logs/sanitize_sequences_{origin}.txt"
log:
"logs/align_{origin}.txt"
benchmark:
@@ -76,7 +77,7 @@ rule align:
python3 scripts/sanitize_sequences.py \
--sequences {input.sequences} \
--strip-prefixes {params.strain_prefixes:q} \
- --output /dev/stdout \
+ --output /dev/stdout 2> {params.sanitize_log} \
| nextalign \
--jobs={threads} \
--reference {input.reference} \
