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| version 1.0 | ||
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| import "./hic.wdl" | ||
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| workflow diploidify { | ||
| meta { | ||
| version: "1.14.0" | ||
| caper_docker: "encodedcc/hic-pipeline:1.14.0" | ||
| caper_singularity: "docker://encodedcc/hic-pipeline:1.14.0" | ||
| } | ||
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| input { | ||
| Array[File] bams | ||
| # This is from genophase, snp.out_HiC.vcf.gz | ||
| File vcf | ||
| File chrom_sizes | ||
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| # Parameters | ||
| Int quality = 30 | ||
| Array[Int] create_diploid_hic_resolutions = [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 200, 100, 50, 20, 10] | ||
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| # Resource params, specify to override the defaults | ||
| Int? merge_num_cpus | ||
| Int? merge_ram_gb | ||
| Int? merge_disk_size_gb | ||
| Int? prepare_bam_num_cpus | ||
| Int? prepare_bam_ram_gb | ||
| Int? prepare_bam_disk_size_gb | ||
| Int? create_diploid_hic_num_cpus | ||
| Int? create_diploid_hic_ram_gb | ||
| Int? create_diploid_hic_disk_size_gb | ||
| Int? create_diploid_dhs_num_cpus | ||
| Int? create_diploid_dhs_ram_gb | ||
| Int? create_diploid_dhs_disk_size_gb | ||
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| String docker = "encodedcc/hic-pipeline:1.14.0" | ||
| String singularity = "docker://encodedcc/hic-pipeline:1.14.0" | ||
| } | ||
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| RuntimeEnvironment runtime_environment = { | ||
| "docker": docker, | ||
| "singularity": singularity | ||
| } | ||
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| call filter_chrom_sizes { input: | ||
| chrom_sizes = chrom_sizes, | ||
| } | ||
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| call hic.merge as merge { input: | ||
| bams = bams, | ||
| num_cpus = merge_num_cpus, | ||
| ram_gb = merge_ram_gb, | ||
| disk_size_gb = merge_disk_size_gb, | ||
| runtime_environment = runtime_environment, | ||
| } | ||
| call prepare_bam { input: | ||
| bam = merge.bam, | ||
| quality = quality, | ||
| chrom_sizes = chrom_sizes, | ||
| num_cpus = prepare_bam_num_cpus, | ||
| ram_gb = prepare_bam_ram_gb, | ||
| disk_size_gb = prepare_bam_disk_size_gb, | ||
| } | ||
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| call create_diploid_hic { input: | ||
| bam = prepare_bam.filtered_bam, | ||
| bam_index = prepare_bam.bam_index, | ||
| vcf = vcf, | ||
| chrom_sizes = filter_chrom_sizes.filtered_chrom_sizes, | ||
| resolutions = create_diploid_hic_resolutions, | ||
| num_cpus = create_diploid_hic_num_cpus, | ||
| ram_gb = create_diploid_hic_ram_gb, | ||
| disk_size_gb = create_diploid_hic_disk_size_gb, | ||
| } | ||
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| call create_diploid_dhs { input: | ||
| bam = prepare_bam.filtered_bam, | ||
| bam_index = prepare_bam.bam_index, | ||
| chrom_sizes = chrom_sizes, | ||
| reads_to_homologs = create_diploid_hic.reads_to_homologs, | ||
| num_cpus = create_diploid_dhs_num_cpus, | ||
| ram_gb = create_diploid_dhs_ram_gb, | ||
| disk_size_gb = create_diploid_dhs_disk_size_gb, | ||
| } | ||
| } | ||
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| task filter_chrom_sizes { | ||
| input { | ||
| File chrom_sizes | ||
| String output_filename = "filtered.chrom.sizes" | ||
| } | ||
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| command <<< | ||
| python3 "$(which filter_chrom_sizes.py)" ~{chrom_sizes} ~{output_filename} | ||
| >>> | ||
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| output { | ||
| File filtered_chrom_sizes = output_filename | ||
| } | ||
| } | ||
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| task prepare_bam { | ||
| input { | ||
| File bam | ||
| File chrom_sizes | ||
| Int quality | ||
| Int num_cpus = 8 | ||
| Int ram_gb = 64 | ||
| Int disk_size_gb = 2000 | ||
| } | ||
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| command <<< | ||
| export CHROM_SIZES_FILENAME="assembly.chrom.sizes" | ||
| mv ~{chrom_sizes} $CHROM_SIZES_FILENAME | ||
| bash /opt/juicer/CPU/diploidify.sh \ | ||
| --from-stage prep \ | ||
| --to-stage prep \ | ||
| --chrom-sizes $CHROM_SIZES_FILENAME \ | ||
| --mapq ~{quality} \ | ||
| --juicer-dir /opt \ | ||
| --phaser-dir /opt/3d-dna \ | ||
| ~{bam} | ||
| >>> | ||
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| output { | ||
| File filtered_bam = "reads.sorted.bam" | ||
| File bam_index = "reads.sorted.bam.bai" | ||
| } | ||
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| runtime { | ||
| cpu: num_cpus | ||
| memory: "~{ram_gb} GB" | ||
| disks: "local-disk ~{disk_size_gb} HDD" | ||
| } | ||
| } | ||
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| task create_diploid_hic { | ||
| input { | ||
| File bam | ||
| File bam_index | ||
| File vcf | ||
| File chrom_sizes | ||
| Array[Int] resolutions | ||
| Int num_cpus = 24 | ||
| Int ram_gb = 128 | ||
| Int disk_size_gb = 2000 | ||
| } | ||
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| command <<< | ||
| mv ~{bam} "reads.sorted.bam" | ||
| mv ~{bam_index} "reads.sorted.bam.bai" | ||
| export CHROM_SIZES_FILENAME="assembly.chrom.sizes" | ||
| mv ~{chrom_sizes} $CHROM_SIZES_FILENAME | ||
| export VCF_FILENAME="snp.vcf" | ||
| gzip -dc ~{vcf} > $VCF_FILENAME | ||
| bash /opt/juicer/CPU/diploidify.sh \ | ||
| --from-stage hic \ | ||
| --to-stage hic \ | ||
| --vcf $VCF_FILENAME \ | ||
| --chrom-sizes $CHROM_SIZES_FILENAME \ | ||
| --resolutions ~{sep="," resolutions} \ | ||
| --threads-hic ~{num_cpus} \ | ||
| --juicer-dir /opt \ | ||
| --phaser-dir /opt/3d-dna | ||
| >>> | ||
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| output { | ||
| # r = reference, a = alternate haplotype but it's arbitrary | ||
| File hic_r = "diploid_inter_r.hic" | ||
| File hic_a = "diploid_inter_a.hic" | ||
| File reads_to_homologs = "reads_to_homologs.txt" | ||
| } | ||
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| runtime { | ||
| cpu: num_cpus | ||
| memory: "~{ram_gb} GB" | ||
| disks: "local-disk ~{disk_size_gb} HDD" | ||
| } | ||
| } | ||
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| task create_diploid_dhs { | ||
| input { | ||
| File bam | ||
| File bam_index | ||
| File chrom_sizes | ||
| File reads_to_homologs | ||
| Int num_cpus = 2 | ||
| Int ram_gb = 128 | ||
| Int disk_size_gb = 1000 | ||
| } | ||
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| command <<< | ||
| mv ~{bam} "reads.sorted.bam" | ||
| mv ~{bam_index} "reads.sorted.bam.bai" | ||
| export CHROM_SIZES_FILENAME="assembly.chrom.sizes" | ||
| mv ~{chrom_sizes} $CHROM_SIZES_FILENAME | ||
| bash /opt/juicer/CPU/diploidify.sh \ | ||
| --from-stage dhs \ | ||
| --to-stage dhs \ | ||
| --chrom-sizes $CHROM_SIZES_FILENAME \ | ||
| --reads-to-homologs ~{reads_to_homologs} \ | ||
| --juicer-dir /opt \ | ||
| --phaser-dir /opt/3d-dna | ||
| >>> | ||
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| output { | ||
| # r = reference, a = alternate haplotype but it's arbitrary | ||
| File bigwig_raw_r = "diploid_inter_raw_r.bw" | ||
| File bigwig_raw_a = "diploid_inter_raw_a.bw" | ||
| File bigwig_corrected_r = "diploid_inter_corrected_r.bw" | ||
| File bigwig_corrected_a = "diploid_inter_corrected_a.bw" | ||
| } | ||
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| runtime { | ||
| cpu: num_cpus | ||
| memory: "~{ram_gb} GB" | ||
| disks: "local-disk ~{disk_size_gb} HDD" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| import argparse | ||
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| def main(): | ||
| parser = get_parser() | ||
| args = parser.parse_args() | ||
| with open(args.chrom_sizes) as chrom_sizes, open( | ||
| args.output_file, "w" | ||
| ) as output_file: | ||
| filter_chrom_sizes(chrom_sizes=chrom_sizes, output_file=output_file) | ||
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| def filter_chrom_sizes(chrom_sizes, output_file): | ||
| for line in chrom_sizes: | ||
| chrom_name = line.split()[0] | ||
| if "_" in chrom_name or chrom_name == "chrEBV": | ||
| continue | ||
| output_file.write(line) | ||
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| def get_parser(): | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument("chrom_sizes") | ||
| parser.add_argument("output_file") | ||
| return parser | ||
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| if __name__ == "__main__": | ||
| main() |
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