53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
# 04b-job-star-extra.yaml
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apiVersion: batch/v1
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kind: Job
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metadata:
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name: star-align-extra
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namespace: rnaseq
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spec:
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backoffLimit: 1
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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: star
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image: quay.io/biocontainers/star:2.7.10a--h9ee0642_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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for acc in ERR458494 ERR458495 ERR458501 ERR458502; do
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echo "=== Aligning $acc ==="
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mkdir -p /data/aligned/$acc
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STAR \
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--runMode alignReads \
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--genomeDir /data/reference/star_index \
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--readFilesIn /data/raw/$acc.fastq.gz \
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--readFilesCommand zcat \
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--outSAMtype BAM SortedByCoordinate \
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--outSAMattributes NH HI AS NM \
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--outFileNamePrefix /data/aligned/$acc/ \
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--runThreadN 4
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done
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echo "=== Done ==="
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for acc in ERR458494 ERR458495 ERR458501 ERR458502; do
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ls -lh /data/aligned/$acc/
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done
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resources:
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requests:
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memory: "6Gi"
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cpu: "4"
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limits:
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memory: "10Gi"
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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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