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March 5, 2019 17:02
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| align = design.combine([8,12,16]) // Cores | |
| .combine([12,32,64]) // Memory (GB) | |
| .combine([1,2,3,7,8,9]) // Method | |
| process alignment { | |
| /* | |
| Alignment as performed identically to the old method | |
| */ | |
| cache 'deep' | |
| tag { gen_tag("alignment", row, meta) } | |
| module 'BWA/0.7.15-intel-2016b:picard/1.107-Java-1.8.0_92:SAMtools/1.3.1-foss-2016b:Sambamba/0.6.6' | |
| memory "${memory} GB" | |
| cpus "${cores}" | |
| publishDir "output/bam/benchmark" | |
| errorStrategy 'finish' | |
| when: | |
| // Only run when there is at least 0.187 Gb/core | |
| cores / memory > 0.187 | |
| input: | |
| set val(row), val(meta), file(fq1), file(fq2), val(cores), val(memory), val(method) from align | |
| output: | |
| set val(row), val(meta), file("${slug}.bam"), file("${slug}.bam.bai") into align_out | |
| script: | |
| // Construct read group | |
| RG = ["@RG", | |
| "ID:${row.sample_name}.${row.seq_sample_id}_${row.run_dir}_${row.lane}", | |
| "SM:${row.sample_name}", | |
| "LB:${row.seq_sample_id}", | |
| "PU:${row.flowcell}.${row.lane}", | |
| "PL:illumina", | |
| "SM:${row.sample_name}"].join("\\t") | |
| meta = new HashMap(meta) | |
| meta['cores'] = cores | |
| meta['memory'] = memory | |
| meta['method'] = method | |
| PICARD_PARAMS = "MAX_RECORDS_IN_RAM=2000000 VALIDATION_STRINGENCY=STRICT" | |
| slug = p(row, meta) | |
| if (method == 1) | |
| """ | |
| # 'Old' method | |
| # Uses the old samtools | |
| module load SAMtools/0.1.19-foss-2016b | |
| bwa mem -t ${task.cpus} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > 35 || \$1 ~ /^@/' - | \\ | |
| samtools view -@ ${task.cpus} -bhS - > out.unsorted.bam | |
| java -d64 -Xmx8g -jar \${ROOTPICARD}/SortSam.jar INPUT=out.unsorted.bam OUTPUT=${slug}.bam SORT_ORDER=coordinate ${PICARD_PARAMS} | |
| java -d64 -Xmx8g -jar \${ROOTPICARD}/BuildBamIndex.jar INPUT=${slug}.bam OUTPUT=${slug}.bam.bai ${PICARD_PARAMS} | |
| """ | |
| else if (method == 2) | |
| """ | |
| # Samtools+sambamba with intermediate file | |
| bwa mem -t ${task.cpus} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' | \\ | |
| samtools view -bh --threads ${task.cpus} - > out.tmp.bam | |
| # Sort alignment | |
| sambamba sort -m "${task.memory.toGiga()}GB" \\ | |
| --nthreads=${task.cpus*params.threads_per_core} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| out.tmp.bam | |
| sambamba index --nthreads=${task.cpus*params.threads_per_core} ${slug}.bam | |
| rm out.tmp.bam | |
| """ | |
| else if (method == 3) | |
| """ | |
| # Samtools+sambamba with intermediate file and balanced threads | |
| bwa mem -t ${task.cpus/2} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' | \\ | |
| samtools view -bh --threads ${task.cpus/2} - > out.tmp.bam | |
| # Sort alignment | |
| sambamba sort -m "${task.memory.toGiga()}GB" \\ | |
| --nthreads=${task.cpus} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| out.tmp.bam | |
| sambamba index --nthreads=${task.cpus} ${slug}.bam | |
| rm out.tmp.bam | |
| """ | |
| else if (method == 4) | |
| """ | |
| # Samtools+sambamba with pipe unbalanced | |
| bwa mem -t ${task.cpus} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' | \\ | |
| samtools view -bh --threads ${task.cpus} - | \\ | |
| sambamba sort -m "${task.memory.toGiga()-2}GB" \\ | |
| --nthreads=${task.cpus} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| /dev/stdin | |
| sambamba index --nthreads=${task.cpus} ${slug}.bam | |
| """ | |
| else if (method == 5) | |
| """ | |
| # Samtools+sambamba with pipe and balanced threads | |
| bwa mem -t ${task.cpus/2} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' | \\ | |
| samtools view -bh --threads ${task.cpus/4} - | \\ | |
| sambamba sort -m "${task.memory.toGiga()-2}GB" \\ | |
| --nthreads=${task.cpus/4} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| /dev/stdin | |
| sambamba index --nthreads=${task.cpus} ${slug}.bam | |
| """ | |
| else if (method == 6) | |
| """ | |
| # Samtools+sambamba with pipe, balanced threads and balanced memory | |
| bwa mem -t ${task.cpus/2} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' | \\ | |
| samtools view -bh --threads ${task.cpus/4} - | \\ | |
| sambamba sort -m "${(task.memory.toGiga()/2)-2}GB" \\ | |
| --nthreads=${task.cpus/4} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| /dev/stdin | |
| sambamba index --nthreads=${task.cpus} ${slug}.bam | |
| """ | |
| else if (method == 7) | |
| """ | |
| # Samtools+sambamba with intermediate file; No threads on samtools out | |
| bwa mem -t ${task.cpus} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' | \\ | |
| samtools view -bh - > out.tmp.bam | |
| # Sort alignment | |
| sambamba sort -m "${task.memory.toGiga()}GB" \\ | |
| --nthreads=${task.cpus*params.threads_per_core} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| out.tmp.bam | |
| sambamba index --nthreads=${task.cpus*params.threads_per_core} ${slug}.bam | |
| rm out.tmp.bam | |
| """ | |
| else if (method == 8) | |
| """ | |
| # BWA Intermediate; Samtools intermediate;Samtools+sambamba with intermediate file; No threads on samtools out | |
| bwa mem -t ${task.cpus} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' > out.SAM | |
| samtools view -bh --threads ${task.cpus} out.SAM > out.tmp.bam | |
| rm out.SAM | |
| # Sort alignment | |
| sambamba sort -m "${task.memory.toGiga()}GB" \\ | |
| --nthreads=${task.cpus*params.threads_per_core} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| out.tmp.bam | |
| sambamba index --nthreads=${task.cpus*params.threads_per_core} ${slug}.bam | |
| rm out.tmp.bam | |
| """ | |
| else if (method == 9) | |
| """ | |
| # BWA Intermediate; Samtools pipe to sambamba | |
| bwa mem -t ${task.cpus} \\ | |
| -R "${RG}" \\ | |
| ${params.genome} ${fq1} ${fq2} | \\ | |
| awk 'length(\$10) > ${params.min_read_length} || \$1 ~ /^@/' > out.SAM | |
| samtools view -bh --threads ${task.cpus} out.SAM > out.tmp.bam | |
| # Sort alignment | |
| sambamba sort -m "${task.memory.toGiga()}GB" \\ | |
| --nthreads=${task.cpus*params.threads_per_core} \\ | |
| --tmpdir=. \\ | |
| --out=${slug}.bam \\ | |
| out.tmp.bam | |
| sambamba index --nthreads=${task.cpus*params.threads_per_core} ${slug}.bam | |
| rm out.tmp.bam out.SAM | |
| """ | |
| } |
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