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Copy pathnon-model-resequencing-diatom-BWA-MEM.yml
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non-model-resequencing-diatom-BWA-MEM.yml
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---
global:
# Initial Directory Setup
- indir: "data/processed"
- outdir: "data/analysis"
# Find Samples
- sample_rule: (Sample.*)$
- find_by_dir: 1
# Output Directory Structure
- by_sample_outdir: 1
# Processed Dirs
- trimmomatic_dir: "data/processed/{$sample}/trimmomatic"
- raw_fastqc_dir: "data/processed/{$sample}"
# Analysis Dirs
- bwa_mem_dir: "data/analysis/{$sample}/bwa_mem"
- samtools_dir: "data/analysis/{$sample}/samtools"
- picard_dir: "data/analysis/{$sample}/picard"
- gatk_dir: "data/analysis/{$sample}/gatk"
- freebayes_dir: "data/analysis/{$sample}/freebayes"
# Tmp Dir - Reference it as the environmental variable TMPDIR
- bwa_mem_tmp_dir: "{$ENV{TMPDIR}}/{$sample}/bwa_mem/tmp"
# Reference Data
- bwa_mem_reference: "/scratch/Reference_Genomes/Public/Plant/Phaeodactylum_tricornutum/NCBI_ASM15095v2/Phaeodactylum_tricornutum.ASM15095v2.dna.toplevel"
- reference: "{$self->bwa_mem_reference}.fa"
# GATK Args
- library: 1
- pcrModel: 0
- goldenVcf: 0
- ploidy: 2
# Shortcuts for long read names
- READ1: "{$self->raw_fastqc_dir}/{$sample}_read1.fastq.gz"
- READ2: "{$self->raw_fastqc_dir}/{$sample}_read2.fastq.gz"
- TR1: "{$self->trimmomatic_dir}/{$sample}_read1_trimmomatic"
- TR2: "{$self->trimmomatic_dir}/{$sample}_read2_trimmomatic"
# HPC Directives
- HPC:
- account: 'gencore'
- partition: 'serial'
- module: 'gencore gencore_dev gencore_variant_detection/1.0'
- cpus_per_task: 1
- commands_per_node: 1
rules:
- bwa_mem:
local:
- indir: "{$self->trimmomatic_dir}"
- outdir: "{$self->bwa_mem_dir}"
- INPUT: "{$self->trimmomatic_dir}/{$sample}"
- OUTPUT: "{$self->bwa_mem_dir}/{$sample}_aligned.sam"
- HPC:
- mem: '60GB'
- cpus_per_task: 12
- walltime: '12:00:00'
process: |
#TASK tags={$sample}
bwa mem -t 12 -M \
{$self->reference} \
{$self->INPUT}_read1_trimmomatic_1PE.fastq.gz \
{$self->INPUT}_read2_trimmomatic_2PE.fastq.gz \
> {$self->OUTPUT}
- samtools_view:
local:
- outdir: "{$self->samtools_dir}"
- INPUT: "{$self->bwa_mem_dir}/{$sample}_aligned.sam"
- OUTPUT: "{$self->samtools_dir}/{$sample}_aligned.bam"
- HPC:
- deps: 'bwa_mem'
- mem: '50GB'
- walltime: '14:00:00'
process: |
#TASK tags={$sample}
samtools view -b -S {$self->INPUT} \
> {$self->OUTPUT}
- picard_cleansam:
local:
- indir: "{$self->samtools_dir}"
- outdir: "{$self->picard_dir}"
- INPUT: "{$self->samtools_dir}/{$sample}_aligned.bam"
- OUTPUT: "{$self->picard_dir}/{$sample}_cleaned.aligned.bam"
- HPC:
- deps: 'samtools_view'
- mem: '50GB'
- walltime: '14:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g CleanSam \
INPUT={$self->INPUT} \
O={$self->OUTPUT} \
TMP_DIR={$self->bwa_mem_tmp_dir}
- picard_sortsam:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->picard_dir}"
- OUTPUT: "{$self->picard_dir}/{$sample}_csorted.cleaned.aligned.bam"
- HPC:
- deps: 'picard_cleansam'
- mem: '50GB'
- walltime: '14:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g SortSam \
INPUT={$self->INPUT} \
O={$self->OUTPUT} \
SO=coordinate \
TMP_DIR={$self->bwa_mem_tmp_dir}
- picard_collect_multiple_metrics:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->picard_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->picard_dir}/{$sample}_collmulmetr.csorted.cleaned.aligned"
- PROGRAM: "PROGRAM=CollectAlignmentSummaryMetrics PROGRAM=CollectInsertSizeMetrics PROGRAM=QualityScoreDistribution PROGRAM=MeanQualityByCycle"
- HPC:
- deps: 'picard_sortsam'
- mem: '25GB'
- walltime: '03:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g CollectMultipleMetrics \
TMP_DIR={$self->bwa_mem_tmp_dir} \
I={$self->INPUT} \
O={$self->OUTPUT} \
{$self->PROGRAM}
- picard_add_or_replace_groups:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->picard_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->picard_dir}/{$sample}_withrg.csorted.cleaned.aligned.bam"
- ARGS: "SORT_ORDER=coordinate RGID=1 RGLB={$self->library} RGPL=illumina RGPU=unit1 RGSM={$sample} RGCN=NYUAD"
- HPC:
- deps: 'picard_sortsam'
- mem: '50GB'
- walltime: '14:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g AddOrReplaceReadGroups \
I={$self->INPUT} \
O={$self->OUTPUT} \
{$self->ARGS}
- picard_bamindex:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->picard_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_withrg.csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->picard_dir}/{$sample}_withrg.csorted.cleaned.aligned.bam"
- HPC:
- deps: 'picard_add_or_replace_groups'
- mem: '50GB'
- walltime: '14:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g BuildBamIndex \
I={$self->INPUT} \
TMP_DIR={$self->bwa_mem_tmp_dir}
- picard_markdups:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->picard_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_withrg.csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->picard_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- metrics_file: "{$self->picard_dir}/{$sample}_markDup_metrics_file.txt"
- HPC:
- deps: 'picard_bamindex'
- mem: '60GB'
- walltime: '20:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g MarkDuplicates \
REMOVE_DUPLICATES=true \
M={$self->metrics_file} \
I={$self->INPUT} \
O={$self->OUTPUT} \
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=100 \
TMP_DIR={$self->bwa_mem_tmp_dir}
- picard_bamindex2:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->picard_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->picard_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- HPC:
- deps: 'picard_markdups'
- mem: '50GB'
- walltime: '12:00:00'
process: |
#TASK tags={$sample}
picard -Xmx2g BuildBamIndex \
I={$self->INPUT} \
TMP_DIR={$self->bwa_mem_tmp_dir}
- samtools_mpileup:
local:
- indir: "{$self->samtools_dir}"
- outdir: "{$self->samtools_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- SAM: "{$self->samtools_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->samtools_dir}/{$sample}_aligned.sorted.vcf.gz"
- HPC:
- deps: 'picard_bamindex2'
- mem: '50GB'
- walltime: '12:00:00'
process: |
#TASK tags={$sample}
rm -rf {$self->OUTPUT} && \
ln -s -f {$self->INPUT} {$self->SAM} && \
samtools index {$self->SAM} && \
samtools mpileup -ugf {$self->reference} \
{$self->INPUT} | bcftools call -vmO z -o \
{$self->OUTPUT}
- tabix_index:
local:
- indir: "{$self->samtools_dir}"
- outdir: "{$self->samtools_dir}"
- INPUT: "{$self->samtools_dir}/{$sample}_aligned.sorted.vcf.gz"
- OUTPUT: "{$self->samtools_dir}/{$sample}_aligned.sorted.vcf.gz"
- HPC:
- deps: 'samtools_mpileup'
- mem: '50GB'
- walltime: '14:00:00'
process: |
#TASK tags={$sample}
tabix -p vcf {$self->INPUT}
- bcftools_stats:
local:
- indir: "{$self->samtools_dir}"
- outdir: "{$self->samtools_dir}"
- INPUT: "{$self->samtools_dir}/{$sample}_aligned.sorted.vcf.gz"
- OUTPUT: "{$self->samtools_dir}/{$sample}_aligned.sorted.vcf.stats"
- HPC:
- deps: 'tabix_index'
- mem: '30GB'
- walltime: '05:00:00'
process: |
#TASK tags={$sample}
bcftools stats -F {$self->reference} -s - {$self->INPUT} \
> {$self->OUTPUT}
- bcftools_filter:
local:
- indir: "{$self->samtools_dir}"
- outdir: "{$self->samtools_dir}"
- INPUT: "{$self->samtools_dir}/{$sample}_aligned.sorted.vcf.gz"
- OUTPUT: "{$self->samtools_dir}/{$sample}_filteredQ10.aligned.sorted.vcf.gz"
- HPC:
- deps: 'tabix_index'
- mem: '60GB'
- walltime: '24:00:00'
process: |
#TASK tags={$sample}
bcftools filter -O z \
-o {$self->OUTPUT} \
-s LOWQUAL -i'%QUAL>10' \
{$self->INPUT}
- freebayes_vcf_calling:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->freebayes_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->freebayes_dir}/{$sample}_freebayes_raw.vcf"
- HPC:
- deps: 'samtools_mpileup'
- mem: '80GB'
- walltime: '28:00:00'
process: |
#TASK tags={$sample}
freebayes -f {$self->reference} \
{$self->INPUT} \
> {$self->OUTPUT}
- freebayes_vcffilter:
local:
- indir: "{$self->freebayes_dir}"
- outdir: "{$self->freebayes_dir}"
- INPUT: "{$self->freebayes_dir}/{$sample}_freebayes_raw.vcf"
- OUTPUT: "{$self->freebayes_dir}/{$sample}_filtered.freebayes.vcf"
- HPC:
- deps: 'freebayes_vcf_calling'
- mem: '50GB'
- walltime: '25:00:00'
process: |
#TASK tags={$sample}
vcffilter -f "QUAL > 1 & QUAL / AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1" \
{$self->INPUT} > {$self->OUTPUT}
- gatk_haplotypecaller:
local:
- indir: "{$self->picard_dir}"
- outdir: "{$self->gatk_dir}"
- INPUT: "{$self->picard_dir}/{$sample}_mdup.withrg.csorted.cleaned.aligned.bam"
- OUTPUT: "{$self->gatk_dir}/{$sample}_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf"
- ARGS: "-stand_emit_conf 10 -stand_call_conf 30 --genotyping_mode DISCOVERY"
- HPC:
- deps: 'picard_bamindex2'
- mem: '80GB'
- walltime: '50:00:00'
- cpus_per_task: 12
process: |
#TASK tags={$sample}
gatk -T HaplotypeCaller \
-nct 12 \
-R {$self->reference} \
-I {$self->INPUT} \
{$self->ARGS} \
-o {$self->OUTPUT}