49 lines
1.5 KiB
YAML
49 lines
1.5 KiB
YAML
# 05-job-featurecounts.yaml
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apiVersion: batch/v1
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kind: Job
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metadata:
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name: featurecounts-v2
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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: featurecounts
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image: quay.io/biocontainers/subread:2.0.6--he4a0461_0
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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 featureCounts on 6 samples ==="
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featureCounts \
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-a /data/reference/annotation.gtf \
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-o /data/counts/gene_counts.txt \
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-T 4 \
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/data/aligned/ERR458493/Aligned.sortedByCoord.out.bam \
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/data/aligned/ERR458494/Aligned.sortedByCoord.out.bam \
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/data/aligned/ERR458495/Aligned.sortedByCoord.out.bam \
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/data/aligned/ERR458500/Aligned.sortedByCoord.out.bam \
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/data/aligned/ERR458501/Aligned.sortedByCoord.out.bam \
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/data/aligned/ERR458502/Aligned.sortedByCoord.out.bam
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echo "=== Done ==="
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cat /data/counts/gene_counts.txt.summary
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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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