Commit dadfba37 authored by Sander Bollen's avatar Sander Bollen
Browse files

fastqc metrics

parent 1ec3d18a
......@@ -287,3 +287,41 @@ rule usable_basenum:
num=out_path("{sample}/bams/{sample}.usable.basenum")
conda: "envs/samtools.yml"
shell: "samtools view -F 4 -F 1024 {input.bam} | cut -f10 | wc -c > {output.num}"
## fastqc
rule fastqc_raw
input:
r1=get_r1
r2=get_r2
params:
odir=out_path("{sample}/pre_process/raw_fastqc")
output:
aux=out_path("{sample}/pre_process/raw_fastqc/.done.txt")
shell: "fastqc -o {params.odir} {input.r1} {input.r2} && echo 'done' > {output.aux}"
rule fastqc_merged
input:
r1=out_path("{sample}/pre_process/{sample}.merged_R1.fastq.gz")
r2=out_path("{sample}/pre_process/{sample}.merged_R2.fastq.gz")
params:
odir=out_path("{sample}/pre_process/merged_fastqc")
output:
aux=out_path("{sample}/pre_process/merged_fastqc/.done.txt")
shell: "fastqc -o {params.odir} {input.r1} {input.r2} && echo 'done' > {output.aux}"
rule fastqc_postqc
input:
r1=out_path("{sample}/pre_process/{sample}.cutadapt_R1.fastq")
r2=out_path("{sample}/pre_process/{sample}.cutadapt_R2.fastq")
params:
odir=out_path("{sample}/pre_process/postqc_fastqc")
output:
aux=out_path("{sample}/pre_process/postqc_fastqc/.done.txt")
shell: "fastqc -o {params.odir} {input.r1} {input.r2} && echo 'done' > {output.aux}"
name: hutspot-fastqc
channels:
- bioconda
- conda-forge
- defaults
- r
dependencies:
- fastqc=0.11.5=pl5.22.0_3
- perl=5.22.0.1=0
- openjdk=8.0.121=1
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