From 4d0cbae9c7304e790cf2dbd17dbb1937a4208b77 Mon Sep 17 00:00:00 2001
From: seehagec01 <seehagec01@fu-berlin.de>
Date: Mon, 21 Mar 2022 18:06:32 +0100
Subject: [PATCH] added qualimap
---
tutorial/workflow/Snakefile | 16 +++++++---------
tutorial/workflow/envs/yourenv.yaml | 1 +
tutorial/workflow/rules/qualimap.smk | 11 +++++++++++
3 files changed, 19 insertions(+), 9 deletions(-)
create mode 100644 tutorial/workflow/rules/qualimap.smk
diff --git a/tutorial/workflow/Snakefile b/tutorial/workflow/Snakefile
index d20a56c..f67a9d2 100644
--- a/tutorial/workflow/Snakefile
+++ b/tutorial/workflow/Snakefile
@@ -6,16 +6,12 @@ samples = pd.read_table(config["samples"], index_col="sample")
rule all:
input:
- expand("results/trimmed/{sample}_forward_paired.fq.gz", sample=samples.index),
- expand("results/trimmed/{sample}_forward_unpaired.fq.gz", sample=samples.index),
- expand("results/trimmed/{sample}_reverse_paired.fq.gz", sample=samples.index),
- expand("results/trimmed/{sample}_reverse_unpaired.fq.gz", sample=samples.index),
- "results/aggregate/mappedcounts.csv",
expand("results/stats/{sample}.stats.txt", sample=samples.index),
- expand("results/fastqc/{sample}_1_fastqc.html", sample=samples.index),
- expand("results/fastqc/{sample}_1_fastqc.zip", sample=samples.index),
- expand("results/fastqc/{sample}_2_fastqc.html", sample=samples.index),
- expand("results/fastqc/{sample}_2_fastqc.zip", sample=samples.index)
+ expand("results/fastqc/trimmed/{sample}_1_fastqc.html", sample=samples.index),
+ expand("results/fastqc/trimmed/{sample}_1_fastqc.zip", sample=samples.index),
+ expand("results/fastqc/trimmed/{sample}_2_fastqc.html", sample=samples.index),
+ expand("results/fastqc/trimmed/{sample}_2_fastqc.zip", sample=samples.index),
+ expand("results/qualimap/{sample}/qualimapReport.html", sample=samples.index)
include:"rules/fastqc.smk"
@@ -26,3 +22,5 @@ include:"rules/samtools.smk"
include:"rules/aggregate.smk"
include:"rules/trimming.smk"
+
+include:"rules/qualimap.smk"
diff --git a/tutorial/workflow/envs/yourenv.yaml b/tutorial/workflow/envs/yourenv.yaml
index 0782b60..5a0ea79 100644
--- a/tutorial/workflow/envs/yourenv.yaml
+++ b/tutorial/workflow/envs/yourenv.yaml
@@ -23,6 +23,7 @@ dependencies:
- perl=5.26.2=h4e221da_0
- pip=21.2.2=py37hecd8cb5_0
- python=3.7.11=h88f2d9e_0
+ - qualimap=2.2.2a
- readline=8.1.2=hca72f7f_1
- samtools=1.3.1=0
- setuptools=58.0.4=py37hecd8cb5_0
diff --git a/tutorial/workflow/rules/qualimap.smk b/tutorial/workflow/rules/qualimap.smk
new file mode 100644
index 0000000..b7d4cda
--- /dev/null
+++ b/tutorial/workflow/rules/qualimap.smk
@@ -0,0 +1,11 @@
+rule qualimap:
+ input:
+ "results/bam_sorted/{sample}.sorted.bam"
+ output:
+ "results/qualimap/{sample}/qualimapReport.html"
+ conda:
+ "../envs/yourenv.yaml"
+ log:
+ "workflow/report/qualimap/{sample}.log"
+ shell:
+ "qualimap bamqc -bam {input} -outdir results/qualimap/{wildcards.sample} 2> {log}"
--
GitLab