Commit 27582b11 authored by Sander Bollen's avatar Sander Bollen
Browse files

fastqc count jobs

parent 1eafc5f0
......@@ -293,7 +293,7 @@ rule usable_basenum:
rule fastqc_raw
input:
r1=get_r1
r1=get_r1,
r2=get_r2
params:
odir=out_path("{sample}/pre_process/raw_fastqc")
......@@ -305,7 +305,7 @@ rule fastqc_raw
rule fastqc_merged
input:
r1=out_path("{sample}/pre_process/{sample}.merged_R1.fastq.gz")
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")
......@@ -317,7 +317,7 @@ rule fastqc_merged
rule fastqc_postqc
input:
r1=out_path("{sample}/pre_process/{sample}.cutadapt_R1.fastq")
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")
......@@ -325,3 +325,23 @@ rule fastqc_postqc
aux=out_path("{sample}/pre_process/postqc_fastqc/.done.txt")
conda: "envs/fastqc.yml"
shell: "fastqc -o {params.odir} {input.r1} {input.r2} && echo 'done' > {output.aux}"
## fastq-count
rule fqcount_preqc:
input:
r1=out_path("{sample}/pre_process/{sample}.merged_R1.fastq.gz"),
r2=out_path("{sample}/pre_process/{sample}.merged_R2.fastq.gz")
output:
out_path("{sample}/pre_process/{sample}.preqc_count.json")
shell: "fastq-count {input.r1} {input.r2} > {output}"
rule fqcount_postqc:
input:
r1=out_path("{sample}/pre_process/{sample}.cutadapt_R1.fastq"),
r2=out_path("{sample}/pre_process/{sample}.cutadapt_R2.fastq")
output:
out_path("{sample}/pre_process/{sample}.postqc_count.json")
shell: "fastq-count {input.r1} {input.r2} > {output}"
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