maximize cores and threads when running pipeline about clockwork HOT 7 CLOSED

clockwork variant_call_one_sample ref_dir out1 reads1_1.fq reads1_2.fq
clockwork variant_call_one_sample ref_dir out2 reads2_1.fq reads2_2.fq
clockwork variant_call_one_sample ref_dir out3 reads3_1.fq reads3_2.fq
... etc

cat commands.txt | parallel -j3 {}

singularity exec clockwork.img clockwork map_reads --unsorted_sam SAMPLENAME Ref.remove_contam/ref.fa SAMPLENAME.sam read1.fastq.gz read2.fastq.gz
singularity exec clockwork.img clockwork remove_contam Ref.remove_contam/remove_contam_metadata.tsv SAMPLENAME.sam SAMPLENAME.decontam.counts.tsv SAMPLENAME.decontam_1.fq.gz SAMPLENAME.decontam_2.fq.gz
singularity exec clockwork.img clockwork variant_call_one_sample --sample_name SAMPLENAME Ref.H37Rv Var_call_SAMPLENAME SAMPLENAME.decontam_1.fq.gz SAMPLENAME.decontam_2.fq.gz

singularity exec clockwork.img clockwork map_reads --unsorted_sam SAMPLENAME2 Ref.remove_contam/ref.fa SAMPLENAME2.sam read1.fastq.gz read2.fastq.gz
singularity exec clockwork.img clockwork remove_contam Ref.remove_contam/remove_contam_metadata.tsv SAMPLENAME2.sam SAMPLENAME2.decontam.counts.tsv SAMPLENAME2.decontam_1.fq.gz SAMPLENAME2.decontam_2.fq.gz
singularity exec clockwork.img clockwork variant_call_one_sample --sample_name SAMPLENAME2 Ref.H37Rv Var_call_SAMPLENAME2 SAMPLENAME2.decontam_1.fq.gz SAMPLENAME2.decontam_2.fq.gz

singularity exec clockwork.img clockwork map_reads --unsorted_sam SAMPLENAME3 Ref.remove_contam/ref.fa SAMPLENAME3.sam read1.fastq.gz read2.fastq.gz
singularity exec clockwork.img clockwork remove_contam Ref.remove_contam/remove_contam_metadata.tsv SAMPLENAME3.sam SAMPLENAME3.decontam.counts.tsv SAMPLENAME3.decontam_1.fq.gz SAMPLENAME3.decontam_2.fq.gz
singularity exec clockwork.img clockwork variant_call_one_sample --sample_name SAMPLENAME3 Ref.H37Rv Var_call_SAMPLENAME3 SAMPLENAME3.decontam_1.fq.gz SAMPLENAME3.decontam_2.fq.gz

process_sample.sh sample_name reads1.fq reads2.fq outdir

name=$1
reads1=$2
reads2=$3
out=$4

singularity exec clockwork.img clockwork map_reads --unsorted_sam $name Ref.remove_contam/ref.fa $out.sam $reads1 $reads2
... etc for the other 2 commands ...

process_sample.sh sample1 reads1_1.fq reads1_2.fq out1
process_sample.sh sample2 reads2_1.fq reads2_2.fq out2
process_sample.sh sample3 reads3_1.fq reads3_2.fq out3
... etc

cat commands.txt | parallel -j3 {}