#!/bin/bash -euo pipefail
STAR \
    --genomeDir STARIndex \
    --readFilesIn AWc_8889_K9me3_1.fq.gz AWc_8889_K9me3_2.fq.gz  \
    --runThreadN 12 \
    --outFileNamePrefix 8889_D_H3K9me3_T1. \
     \
    --outSAMattrRGline ID:8889_D_H3K9me3_T1 'SM:8889_D_H3K9me3_T1' \
    --runMode alignReads --alignIntronMax 1 --alignEndsType EndToEnd --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outSAMattributes NH HI AS NM MD

if [ -f 8889_D_H3K9me3_T1.Unmapped.out.mate1 ]; then
    mv 8889_D_H3K9me3_T1.Unmapped.out.mate1 8889_D_H3K9me3_T1.unmapped_1.fastq
    gzip 8889_D_H3K9me3_T1.unmapped_1.fastq
fi
if [ -f 8889_D_H3K9me3_T1.Unmapped.out.mate2 ]; then
    mv 8889_D_H3K9me3_T1.Unmapped.out.mate2 8889_D_H3K9me3_T1.unmapped_2.fastq
    gzip 8889_D_H3K9me3_T1.unmapped_2.fastq
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_STAR:STAR_ALIGN":
    star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS