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Merge pull request #1067 from maxplanck-ie/pairtools_merge
Pairtools merge
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -19,4 +19,4 @@ max_thread: 25 | |
| #print tools versions | ||
| toolsVersion: True | ||
| oldConfig: | ||
| configMode: manual | ||
| configMode: manual | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,199 +1,167 @@ | ||
| # based on https://github.com/caballero/snakemake-pairtools-phased/tree/df410ff | ||
| rule generate_chromsizes: | ||
| input: | ||
| genome_index | ||
| output: | ||
| 'genome/genome.chromsizes' | ||
| threads: 1 | ||
| shell:''' | ||
| cut -f1,2 {input} > {output} | ||
| ''' | ||
|
|
||
|
|
||
| # Define function that returns pair files (phased or unphased), based on the reference. | ||
| def ret_pair(wildcards): | ||
| if "diploid_genome" in wildcards.ref: | ||
| # Phased setting | ||
| return f"pairs/{wildcards.sample}.{wildcards.ref}_phased.pairs.gz" | ||
| else: | ||
| return f"pairs/{wildcards.sample}.{wildcards.ref}.pairs.gz" | ||
|
|
||
|
|
||
| # different to bwa.snakefile | ||
| # here we skip the expensive sorting with samtools after bwa mem | ||
| # consider making this optional in bwa.snakefile | ||
| rule bwa_mapping: | ||
| input: | ||
| fq1="FASTQ_fastp/{sample}_R1.fastq.gz", | ||
| fq2="FASTQ_fastp/{sample}_R2.fastq.gz", | ||
| ix="genome/{ref}.fa.gz.bwt", | ||
| fq2="FASTQ_fastp/{sample}_R2.fastq.gz" | ||
| output: | ||
| bam="bam/{sample}.{ref}.bam", | ||
| bam="bam/{sample}.bam", | ||
| threads: 30 | ||
| params: | ||
| bwathreads=config["alignerThreads"], | ||
| bwaparams=config["alignerOptions"], | ||
| fna=lambda wildcards, input: Path(input.ix).with_suffix(""), | ||
| bwa_index = bwa_index | ||
| resources: | ||
| mem_mb=3000, | ||
| benchmark: | ||
| "bam/.benchmark/bwa_mapping.{sample}.{ref}.benchmark" | ||
| "bam/.benchmark/bwa_mapping.{sample}.benchmark" | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| bwa mem \ | ||
| {params.bwaparams} \ | ||
| -t {params.bwathreads} \ | ||
| {params.fna} \ | ||
| -t 22 \ | ||
| {params.bwa_index} \ | ||
| {input.fq1} \ | ||
| {input.fq2} \ | ||
| | samtools view -@ 8 -b \ | ||
| > {output.bam} | ||
| """ | ||
|
|
||
|
|
||
| rule pairtools_parse: | ||
| input: | ||
| bam="bam/{sample}.{ref}.bam", | ||
| chr_sizes="genome/{ref}.chromsizes", | ||
| bam="bam/{sample}.bam", | ||
| chr_sizes='genome/genome.chromsizes' | ||
| output: | ||
| pairs="pairs/{sample}.{ref}.pairs.gz", | ||
| pairs=temp("pairs/{sample}.unsorted.pairs.gz"), | ||
| params: | ||
| minmapq=40, | ||
| cols=lambda wildcards: ( | ||
| "--add-columns XB,AS,XS" if "diploid_genome" in wildcards.ref else "" | ||
| ), | ||
| minmapq=40 | ||
| threads: 12 | ||
| benchmark: | ||
| "pairs/.benchmark/pairtools_parse.{sample}.{ref}.benchmark" | ||
| "pairs/.benchmark/pairtools_parse.{sample}.benchmark" | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| pairtools parse \ | ||
| --min-mapq {params.minmapq} \ | ||
| {params.cols} \ | ||
| --drop-sam \ | ||
| --walks-policy 5unique \ | ||
| -c {input.chr_sizes} \ | ||
| {input.bam} \ | ||
| -o {output.pairs} | ||
| """ | ||
|
|
||
|
|
||
| rule pairtools_phase: | ||
| input: | ||
| pairs="pairs/{sample}.diploid_genome.pairs.gz", | ||
| output: | ||
| pairs="pairs/{sample}.diploid_genome_phased.pairs.gz", | ||
| params: | ||
| hap1=strains[0], | ||
| hap2=strains[1], | ||
| threads: 12 | ||
| benchmark: | ||
| "pairs/.benchmark/pairtools_phase.{sample}.benchmark" | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| pairtools phase \ | ||
| --phase-suffixes _{params.hap1} _{params.hap2} \ | ||
| --tag-mode XB \ | ||
| --clean-output \ | ||
| {input.pairs} -o {output.pairs} | ||
| """ | ||
|
|
||
|
|
||
| rule pairtools_sort: | ||
| input: | ||
| ret_pair, | ||
| pairs = "pairs/{sample}.unsorted.pairs.gz", | ||
| output: | ||
| pairs="pairs/{sample}.{ref}.pairs.sorted.gz", | ||
| pairs = "pairs/{sample}.pairs.gz", | ||
| threads: 20 | ||
| benchmark: | ||
| "pairs/.benchmark/pairtools_sort.{sample}.{ref}.benchmark" | ||
| "pairs/.benchmark/pairtools_sort.{sample}.benchmark" | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| pairtools sort \ | ||
| {input} \ | ||
| {input.pairs} \ | ||
| -o {output.pairs} \ | ||
| --memory 20G | ||
| """ | ||
|
|
||
|
|
||
| rule pairtools_dedup: | ||
| input: | ||
| pairs="pairs/{sample}.{ref}.pairs.sorted.gz", | ||
| pairs="pairs/{sample}.pairs.gz", | ||
| output: | ||
| pairs="pairs/{sample}.{ref}.pairs.dedup.gz", | ||
| stats="pairs/{sample}.{ref}.pairs.dedup.stats", | ||
| params: | ||
| extra_cols=lambda wildcards: ( | ||
| "--extra-col-pair phase1 phase2" if "diploid" in wildcards.ref else "" | ||
| ), | ||
| pairs="pairs/{sample}.pairs.dedup.gz", | ||
| stats="pairs/{sample}.pairs.dedup.stats" | ||
| threads: 12 | ||
| benchmark: | ||
| "pairs/.benchmark/pairtools_dedup.{sample}.{ref}.benchmark" | ||
| "pairs/.benchmark/pairtools_dedup.{sample}.benchmark" | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| pairtools dedup \ | ||
| --mark-dups \ | ||
| {params.extra_cols} \ | ||
| --output-dups - \ | ||
| --output-unmapped - \ | ||
| --output-stats {output.stats} \ | ||
| -o {output.pairs} \ | ||
| {input.pairs} | ||
| """ | ||
|
|
||
| rule pairix: | ||
| input: | ||
| pairs = 'pairs/{sample}.pairs.dedup.gz' | ||
| output: | ||
| ix = 'pairs/{sample}.pairs.dedup.gz.px2' | ||
| threads: 2 | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| pairix -f -p pairs {input.pairs} | ||
| """ | ||
|
|
||
| rule pairtools_filter_phased: | ||
| rule cooler: | ||
| input: | ||
| pairs="pairs/{sample}.diploid_genome.pairs.dedup.gz", | ||
| pairs = 'pairs/{sample}.pairs.dedup.gz', | ||
| ix = 'pairs/{sample}.pairs.dedup.gz.px2', | ||
| chromsizes = 'genome/genome.chromsizes' | ||
| output: | ||
| stats="phase_stats/{sample}.diploid_genome_{phasetype}.pairs.stats", | ||
| pairs="phase_stats/{sample}.diploid_genome_{phasetype}.pairs.gz", | ||
| params: | ||
| filterparam=lambda wildcards: PHASEDIC[wildcards.phasetype], | ||
| resources: | ||
| mem_mb=1000, | ||
| benchmark: | ||
| "phase_stats/.benchmark/pairtools_filter_phased.{sample}.diploid_genome_{phasetype}.benchmark" | ||
| threads: 12 | ||
| cool = 'cooler/{sample}.5000.cool' | ||
| threads: 20 | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| pairtools select \ | ||
| '{params.filterparam}' \ | ||
| {input.pairs} \ | ||
| -o {output.pairs} | ||
| pairtools stats {output.pairs} -o {output.stats} | ||
| cooler cload pairix -p {threads} {input.chromsizes}:5000 {input.pairs} {output.cool} | ||
| cooler balance --nproc {threads} {output.cool} | ||
| """ | ||
|
|
||
| rule mcool: | ||
| input: | ||
| cool = 'cooler/{sample}.5000.cool' | ||
| output: | ||
| mcool = 'cooler/{sample}.5000.mcool' | ||
| threads: 20 | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| cooler zoomify --resolutions 5000,10000,20000,40000,80000,120000 --balance --nproc {threads} {input.cool} | ||
| """ | ||
|
|
||
| rule multiqc: | ||
| input: | ||
| stats=expand( | ||
| "pairs/{sample}.{ref}.pairs.dedup.stats", sample=samples, ref=REFERENCES | ||
| ), | ||
| phasedstats=expand( | ||
| "phase_stats/{sample}.diploid_genome_{phasetype}.pairs.stats", | ||
| sample=samples, | ||
| phasetype=PHASEDIC.keys(), | ||
| ), | ||
| cools=expand( | ||
| 'cooler/{sample}.5000.mcool', sample=samples | ||
| ) | ||
| output: | ||
| html="multiqc/multiqc_report.html", | ||
| html="multiQC/multiqc_report.html", | ||
| params: | ||
| odir="multiqc", | ||
| odir="multiQC", | ||
| benchmark: | ||
| "multiqc/.benchmark/multiqc.benchmark" | ||
| "multiQC/.benchmark/multiqc.benchmark" | ||
| threads: 1 | ||
| conda: | ||
| CONDA_MAKEPAIRS_ENV | ||
| shell: | ||
| """ | ||
| echo input: {input.phasedstats} | ||
| multiqc \ | ||
| --module pairtools \ | ||
| --module fastqc \ | ||
| --module fastp \ | ||
| -o {params.odir} \ | ||
| . | ||
| """ | ||
| """ |
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