Commit fcfa28c2 authored by van den Berg's avatar van den Berg
Browse files

Update multiqc, add logfile to cutadapt

parent b8934d0a
......@@ -71,7 +71,7 @@ containers = {
"fastq-count": "docker://quay.io/biocontainers/fastq-count:0.1.0--h14c3975_0",
"fastqc": "docker://quay.io/biocontainers/fastqc:0.11.7--4",
"gatk": "docker://broadinstitute/gatk3:3.7-0",
"multiqc": "docker://quay.io/biocontainers/multiqc:1.5--py36_0",
"multiqc": "docker://quay.io/biocontainers/multiqc:1.8--py_2",
"picard-2.14": "docker://quay.io/biocontainers/picard:2.14--py36_0",
"python3": "docker://python:3.6-slim",
"samtools-1.7-python-3.6": "docker://quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:1abf1824431ec057c7d41be6f0c40e24843acde4-0",
......@@ -142,13 +142,14 @@ rule cutadapt:
output:
r1 = "{sample}/pre_process/{sample}-{read_group}_R1.fastq.gz",
r2 = "{sample}/pre_process/{sample}-{read_group}_R2.fastq.gz",
summary = "{sample}/pre_process/{sample}-{read_group}.txt"
log:
"{sample}/pre_process/{sample}-{read_group}.txt"
singularity: containers["cutadapt"]
shell: "cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG "
"--minimum-length 1 --quality-cutoff=20,20 "
"--output {output.r1} --paired-output {output.r2} -Z "
"{input.r1} {input.r2} "
"--report=minimal > {output.summary}"
"--report=minimal > {log}"
rule align:
"""Align fastq files"""
......
......@@ -192,6 +192,7 @@
- name: test-integration-two-readgroups
tags:
- integration
- new
command: >
snakemake
--use-singularity
......@@ -219,6 +220,8 @@
- path: "micro/pre_process/raw-micro-lib_01/micro_rg1_R2_fastqc.zip"
- path: "micro/pre_process/raw-micro-lib_02/micro_rg2_R1_fastqc.zip"
- path: "micro/pre_process/raw-micro-lib_02/micro_rg2_R2_fastqc.zip"
- path: "micro/pre_process/micro-lib_01.txt"
- path: "micro/pre_process/micro-lib_02.txt"
- path: "micro/coverage/covstats.json"
contains:
......
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