process sort_bam (with sample) inputs file MAPPED_READS_DIR / sample "_Aligned.out.bam" outputs . bam: file MAPPED_READS_DIR / sample "_Aligned.sortedByCoord.out.bam" . log: file LOG_DIR / "samtools_sort_" sample ".log" packages . "samtools" . "coreutils" # { mkdir -p {{LOG_DIR}} {{SAMTOOLS_EXEC}} sort -o {{outputs:bam}} {{inputs}} >> {{outputs:log}} 2>&1 }