44 lines
1.0 KiB
YAML
44 lines
1.0 KiB
YAML
# 03-job-fastqc.yaml
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apiVersion: batch/v1
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kind: Job
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metadata:
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name: fastqc
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namespace: rnaseq
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spec:
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backoffLimit: 2
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template:
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spec:
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restartPolicy: Never
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containers:
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- name: fastqc
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image: biocontainers/fastqc:v0.11.9_cv8
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command: ["/bin/sh", "-c"]
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args:
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- |
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set -e
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echo "=== Running FastQC on all samples ==="
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fastqc \
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/data/raw/ERR458493.fastq.gz \
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/data/raw/ERR458500.fastq.gz \
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--outdir /data/fastqc \
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--threads 4
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echo "=== Done ==="
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ls -lh /data/fastqc/
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resources:
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requests:
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memory: "1Gi"
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cpu: "2"
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limits:
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memory: "2Gi"
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cpu: "4"
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volumeMounts:
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- name: workspace
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mountPath: /data
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volumes:
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- name: workspace
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persistentVolumeClaim:
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claimName: rnaseq-workspace
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