File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/8cd05e59914d22bce2e98f8972c22d/.command.sh
Size
1.6 KB
Task
DAQ:SAMTOOLS_MERGE (1047_JG-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam##idx##1047_JG-T1-TDNA-1_A23MHWWLT4_1.bai \
    1/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 2/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 3/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 4/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 5/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 6/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 7/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 8/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 9/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 10/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 11/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 12/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 13/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 14/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 15/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 16/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 17/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 18/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 19/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 20/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 21/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 22/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 23/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 24/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 25/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 26/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 27/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 28/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 29/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 30/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 31/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam 32/1047_JG-T1-TDNA-1_A23MHWWLT4_1.bam

# Touch index to ensure timestamp is newer than aligned file
touch 1047_JG-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