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WIP: TODOs
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joverlee521 committed Jul 20, 2024
1 parent fd9d7e1 commit bc434d0
Showing 1 changed file with 10 additions and 1 deletion.
11 changes: 10 additions & 1 deletion workflow/snakemake_rules/nextclade.smk
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,16 @@ rule create_empty_nextclade_aligned:
benchmark:
f"benchmarks/create_empty_nextclade_aligned_{database}.txt"

# XXX TODO for ignoring cache on version changes
# Same steps below need to be applied to `download_nextclade_tsv_from_s3` and `download_previous_alignment_from_s3`
# 1. Require "nextclade" as input - used to output version
# 2. Save Nextclade dataset version
# - dataset_version="$(unzip -p {input.dataset} pathogen.json | jq -r '.version.tag')"
# - need to make {dataset_name} -> {reference} wildcard change
# 3. Check Nextclade version against cache output - just check first row as representative of full file
# - nextclade_version
# - dataset_version
# 4. If either nextclade_version or dataset_version don't match then output empty file to ignore cache

# Only include rules to fetch from S3 if S3 config params are provided
if config.get("s3_dst") and config.get("s3_src"):
Expand Down Expand Up @@ -108,7 +118,6 @@ if config.get("s3_dst") and config.get("s3_src"):
touch {output.alignment}
"""


rule get_sequences_without_nextclade_annotations:
"""Find sequences in FASTA which don't have clades assigned yet"""
input:
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