From d75cd8beb5edb0a5298903e8ce270a9f7f399664 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<nicolas.fernandez@ird.fr>
Date: Fri, 10 Jan 2025 16:58:15 +0100
Subject: [PATCH] Fix: l.544 pass 'reference' as input (not params)
---
workflow/Snakefile | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/workflow/Snakefile b/workflow/Snakefile
index d4ed95e..4eff7a1 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -540,20 +540,19 @@ rule bedtools_masking:
"""
conda:
BEDTOOLS
- params:
- path = REF_PATH
input:
+ reference = "resources/genomes/{reference}.fasta",
low_cov_mask = "results/03_Coverage/{reference}/bed/{sample}_{aligner}_{min_cov}X_low-cov-mask.bed"
output:
masked_ref = "results/04_Variants/{reference}/{sample}_{aligner}_{min_cov}X_masked-ref.fasta"
log:
"results/10_Reports/tools-log/bedtools/{reference}/{sample}_{aligner}_{min_cov}X_masking.log"
shell:
- "bedtools maskfasta " # Bedtools maskfasta, mask a fasta file based on feature coordinates
- "-fi {params.path}{wildcards.reference}.fasta " # Input FASTA file
- "-bed {input.low_cov_mask} " # BED/GFF/VCF file of ranges to mask in -fi
- "-fo {output.masked_ref} " # Output masked FASTA file
- "&> {log}" # Log redirection
+ "bedtools maskfasta " # Bedtools maskfasta, mask a fasta file based on feature coordinates
+ "-fi {input.reference} " # Input FASTA file
+ "-bed {input.low_cov_mask} " # BED/GFF/VCF file of ranges to mask in -fi
+ "-fo {output.masked_ref} " # Output masked FASTA file
+ "&> {log}" # Log redirection
###############################################################################
rule bedtools_merged_mask:
--
GitLab