From 3631fcbfd247cf3d6390d41491c275f7217e6485 Mon Sep 17 00:00:00 2001
From: kdc715 <kedic@LIT-PF3VB193.localdomain>
Date: Thu, 13 Feb 2025 17:20:20 +0100
Subject: [PATCH] fix analysis after contamination removal
---
snakemodules/analysis.smk | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/snakemodules/analysis.smk b/snakemodules/analysis.smk
index a32b477..3241b55 100644
--- a/snakemodules/analysis.smk
+++ b/snakemodules/analysis.smk
@@ -52,9 +52,9 @@ if config["SICKLE"]=="no":
if config["remove_contamination"]=="yes":
rule email_unmapped_analysis_no_filtler_after_clean:
input:
- single=expand("{p}/{s}/single.fastq", p=WORK_DIR, s=SAMPLES),
- paired1=expand("{p}/{s}/paired.1.fastq", p=WORK_DIR, s=SAMPLES),
- paired2=expand("{p}/{s}/paired.2.fastq", p=WORK_DIR, s=SAMPLES)
+ single=expand("{p}/{s}/single_clean.fastq", p=WORK_DIR, s=SAMPLES),
+ paired1=expand("{p}/{s}/paired_1_clean.fastq", p=WORK_DIR, s=SAMPLES),
+ paired2=expand("{p}/{s}/paired_2_clean.fastq", p=WORK_DIR, s=SAMPLES)
output:
notify_file=temp("notify/unmapped_analysis_no_filtler_after_clean.txt")
params:
@@ -78,9 +78,9 @@ if config["SICKLE"]=="no":
rule unmapped_analysis_no_filtler_after_clean:
input:
notify="notify/unmapped_analysis_no_filtler_after_clean.txt",
- single=expand("{p}/{s}/single.fastq", p=WORK_DIR, s=SAMPLES),
- paired1=expand("{p}/{s}/paired.1.fastq", p=WORK_DIR, s=SAMPLES),
- paired2=expand("{p}/{s}/paired.2.fastq", p=WORK_DIR, s=SAMPLES)
+ single=expand("{p}/{s}/single_clean.fastq", p=WORK_DIR, s=SAMPLES),
+ paired1=expand("{p}/{s}/paired_1_clean.fastq", p=WORK_DIR, s=SAMPLES),
+ paired2=expand("{p}/{s}/paired_2_clean.fastq", p=WORK_DIR, s=SAMPLES)
output:
RESULTS_DIR + "/read_numbers_no_sickle_after_clean.png"
conda:
--
GitLab