rule indelrealigner:
    input: bam="{base}.bam",intervals="{base}.intervals",bai='{base}.bam.bai'
    output: bam=temp("{base} realigned.bam")
    params: batch="-q ccr -l nodes=1:gpfs"
    threads: 1
    shell: "touch {output:q}"

rule realignertargetcreator:
    input: "{base}.bam", "{base}.bam.bai"
    output: temp("{base}.intervals")
    params: batch="-q ccr -l nodes=1:gpfs"
    threads: 32
    shell: "touch {output:q}"


rule indexbam:
    threads: 1
    input: '{base}.bam'
    output: temp('{base}.bam.bai')
    params: batch="-q ccr -l nodes=1:gpfs"
    shell: 'touch {output:q}'
