Update mapping process - samtools pipe after bwa introduces inefficiency

[cgpu]

As discussed w/ @afonsoguerra the hybrid bwa | samtools command introduces an important inefficiency that translates to significant increase of execution time

GenomeChronicler-Sarek-nf/main.nf

Lines 677 to 679 in b7d4713

	${convertToFastq}
	bwa mem -K 100000000 -R \"${readGroup}\" ${extra} -t ${task.cpus} -M ${fasta} \
	${input} | samtools sort - > ${idSample}_${idRun}.bam

ToDo:

• Update command in main.nf
• Add explicit resource allocation in nextflow.config [merge cgpu fork]

Also, yeahie 🎉 for inaugural PGP issue!