rna_fq2bam

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# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
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docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun rna_fq2bam \
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    --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2} \
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    --genome-lib-dir /workdir/${PATH_TO_GENOME_LIBRARY}/ \
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    --output-dir /outputdir/${PATH_TO_OUTPUT_DIRECTORY} \
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    --ref /workdir/${REFERENCE_FILE} \
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    --out-bam /outputdir/${OUTPUT_BAM} \
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    --read-files-command zcat

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# STAR Alignment
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$ ./STAR \
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      --genomeDir <INPUT_DIR>/${PATH_TO_GENOME_LIBRARY} \
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      --readFilesIn <INPUT_DIR>/${INPUT_FASTQ_1} <INPUT_DIR>/${INPUT_FASTQ_2} \
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      --outFileNamePrefix <OUTPUT_DIR>/${PATH_TO_OUTPUT_DIRECTORY}/ \
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      --outSAMtype BAM SortedByCoordinate \
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      --readFilesCommand zcat
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# Mark Duplicates
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$ gatk MarkDuplicates \
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    --java-options -Xmx30g \
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    -I Aligned.sortedByCoord.out.bam \ # This filename is determined by STAR.
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    -O <OUTPUT_DIR>/${NAME_OF_OUTPUT_BAM_FILE} \
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    -M metrics.txt

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# Add this line in ReadAlign::quantTranscriptome() function in ReadAlign_quantTranscriptome.cpp
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rngMultOrder.seed(777);
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# Add it right before:
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alignT[int(rngUniformReal0to1(rngMultOrder)*nAlignT)].primaryFlag=true;