Commit 96b8a6d8 authored by Sander Bollen's avatar Sander Bollen
Browse files

use fastqc version 0.11.7 for singularity

parent 5f7a0893
Pipeline #2614 failed with stages
in 5 minutes and 59 seconds
......@@ -493,7 +493,11 @@ rule usable_basenum:
## fastqc
rule fastqc_raw:
"""Run fastqc on raw fastq files"""
"""
Run fastqc on raw fastq files
NOTE: singularity version uses 0.11.7 in stead of 0.11.5 due to
perl missing in the container of 0.11.5
"""
input:
r1=get_r1,
r2=get_r2
......@@ -501,14 +505,18 @@ rule fastqc_raw:
odir="{sample}/pre_process/raw_fastqc"
output:
aux="{sample}/pre_process/raw_fastqc/.done.txt"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.5--1"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
conda: "envs/fastqc.yml"
shell: "fastqc --nogroup -o {params.odir} {input.r1} {input.r2} "
"&& echo 'done' > {output.aux}"
rule fastqc_merged:
"""Run fastqc on merged fastq files"""
"""
Run fastqc on merged fastq files
NOTE: singularity version uses 0.11.7 in stead of 0.11.5 due to
perl missing in the container of 0.11.5
"""
input:
r1="{sample}/pre_process/{sample}.merged_R1.fastq.gz",
r2="{sample}/pre_process/{sample}.merged_R2.fastq.gz",
......@@ -518,14 +526,18 @@ rule fastqc_merged:
output:
r1="{sample}/pre_process/merged_fastqc/{sample}.merged_R1_fastqc.zip",
r2="{sample}/pre_process/merged_fastqc/{sample}.merged_R2_fastqc.zip"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.5--1"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
conda: "envs/fastqc.yml"
shell: "bash {input.fq} {input.r1} {input.r2} "
"{output.r1} {output.r2} {params.odir}"
rule fastqc_postqc:
"""Run fastqc on fastq files post pre-processing"""
"""
Run fastqc on fastq files post pre-processing
NOTE: singularity version uses 0.11.7 in stead of 0.11.5 due to
perl missing in the container of 0.11.5
"""
input:
r1="{sample}/pre_process/{sample}.cutadapt_R1.fastq",
r2="{sample}/pre_process/{sample}.cutadapt_R2.fastq",
......@@ -535,7 +547,7 @@ rule fastqc_postqc:
output:
r1="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip",
r2="{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R2_fastqc.zip"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.5--1"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
conda: "envs/fastqc.yml"
shell: "bash {input.fq} {input.r1} {input.r2} "
"{output.r1} {output.r2} {params.odir}"
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment