File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/efd16529d13104243b107dd6dcea07/.command.sh
Size
767 bytes
Task
DAQ:SAMTOOLS_MERGE (1136_4Z5-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam##idx##1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bai \
    1/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 2/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 3/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 4/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 5/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 6/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 7/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam 8/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bam

# Touch index to ensure timestamp is newer than aligned file
touch 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.bai

cat <<-END_VERSIONS > versions.yml
"DAQ:SAMTOOLS_MERGE":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS