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Quality Control

The quality control module removes adapters, trims and filters short read and long read data.

Input

-entry wShortReadQualityControl -params-file example_params/qc.yml

Warning

The configuration file shown here is for demonstration and testing purposes only. Parameters that should be used in production can be viewed in the quality control section of one of the yaml files located in the default folder of the Toolkit's Github repository.

tempdir: "tmp"
summary: false
s3SignIn: false
output: "output"
logDir: log
runid: 1
databases: "/mnt/databases"
logLevel: 1
scratch: "/vol/scratch"
steps:
  qc:
    input: "test_data/qc/reads_split.tsv"
    fastp:
       # Example params: " --cut_front --cut_tail --detect_adapter_for_pe  "
       additionalParams: "  "
    filterHuman:
      additionalParams: "  "
      database:
        download:
          source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/human_filter.db.20231218v2.gz
          md5sum: cc92c0f926656565b1156d66a0db5a3c
resources:
  highmemLarge:
    cpus: 28
    memory: 230
  highmemMedium:
    cpus: 14
    memory: 113
  large:
    cpus: 28
    memory: 58
  medium:
    cpus: 14
    memory: 29
  small:
    cpus: 7
    memory: 14
  tiny:
    cpus: 1
    memory: 1

-entry wOntQualityControl -params-file example_params/qcONT.yml

SAMPLE  READS1  READS2
test1   https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/small/read1_1.fq.gz  https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/small/read2_1.fq.gz
test2   https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/small/read1_1.fq.gz  https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/small/read2_1.fq.gz

SAMPLE  READS
nano    https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/meta_test/SRR16328449_qc.fq.gz

Output

The output is a gzipped fastq file (short read: SAMPLE_interleaved.qc.fq.gz, long read: SAMPLE_qc.fq.gz) containing trimmed and quality filtered reads.