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Commit 4d0cbae9 authored by seehagec01's avatar seehagec01
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added qualimap

parent afac6484
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...@@ -6,16 +6,12 @@ samples = pd.read_table(config["samples"], index_col="sample") ...@@ -6,16 +6,12 @@ samples = pd.read_table(config["samples"], index_col="sample")
rule all: rule all:
input: 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/stats/{sample}.stats.txt", sample=samples.index),
expand("results/fastqc/{sample}_1_fastqc.html", sample=samples.index), expand("results/fastqc/trimmed/{sample}_1_fastqc.html", sample=samples.index),
expand("results/fastqc/{sample}_1_fastqc.zip", sample=samples.index), expand("results/fastqc/trimmed/{sample}_1_fastqc.zip", sample=samples.index),
expand("results/fastqc/{sample}_2_fastqc.html", sample=samples.index), expand("results/fastqc/trimmed/{sample}_2_fastqc.html", sample=samples.index),
expand("results/fastqc/{sample}_2_fastqc.zip", 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" include:"rules/fastqc.smk"
...@@ -26,3 +22,5 @@ include:"rules/samtools.smk" ...@@ -26,3 +22,5 @@ include:"rules/samtools.smk"
include:"rules/aggregate.smk" include:"rules/aggregate.smk"
include:"rules/trimming.smk" include:"rules/trimming.smk"
include:"rules/qualimap.smk"
...@@ -23,6 +23,7 @@ dependencies: ...@@ -23,6 +23,7 @@ dependencies:
- perl=5.26.2=h4e221da_0 - perl=5.26.2=h4e221da_0
- pip=21.2.2=py37hecd8cb5_0 - pip=21.2.2=py37hecd8cb5_0
- python=3.7.11=h88f2d9e_0 - python=3.7.11=h88f2d9e_0
- qualimap=2.2.2a
- readline=8.1.2=hca72f7f_1 - readline=8.1.2=hca72f7f_1
- samtools=1.3.1=0 - samtools=1.3.1=0
- setuptools=58.0.4=py37hecd8cb5_0 - setuptools=58.0.4=py37hecd8cb5_0
......
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}"
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