File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/e1e86a21e09b786bc33d1ddf0dcdf3/.command.sh
Size
756 bytes
Task
DAQ:SAMTOOLS_MERGE (659_d0M-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam##idx##659_d0M-T1-TDNA-1_A23MHWWLT4_1.bai \
    1/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 2/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 3/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 4/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 5/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 6/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 7/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam 8/659_d0M-T1-TDNA-1_A23MHWWLT4_1.bam

# Touch index to ensure timestamp is newer than aligned file
touch 659_d0M-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