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Added merge_original_and_split_bam_sort_all_reads_name_and_position
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@ekiernan
ekiernan committed Oct 25, 2023
1 parent 055a9ba commit 26347b5
Showing 1 changed file with 97 additions and 67 deletions.
164 changes: 97 additions & 67 deletions beta-pipelines/skylab/m3c/CondensedSnm3C.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -52,16 +52,16 @@ workflow WDLized_snm3C {
genome_fa = genome_fa
}

call remove_overlap_read_parts {
input:
bam = Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.merge_sorted_bam_tar
}
call remove_overlap_read_parts {
input:
bam = Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.merge_sorted_bam_tar
}

# call merge_original_and_split_bam_and_sort_all_reads_by_name_and_position {
# input:
# unique_bam = separate_unmapped_reads.unique_bam,
# split_bam = remove_overlap_read_parts.remove_overlap_bam
# }
call merge_original_and_split_bam_and_sort_all_reads_by_name_and_position {
input:
bam = Separate_unmapped_reads.unique_bam_tar,
split_bam = remove_overlap_read_parts.output_bam_tar
}
#
# call call_chromatin_contacts {
# input:
Expand Down Expand Up @@ -101,7 +101,6 @@ workflow WDLized_snm3C {
#File MappingSummary = summary.MappingSummary
#File allcFiles = unique_reads_allc.
#File allc_CGNFiles = unique_reads_cgn_extraction.
#File bamFiles = merge_original_and_split_bam_and_sort_all_reads_by_name_and_position.name_sorted_bam
#File UniqueAlign_cell_parser_picard_dedup = dedup_unique_bam_and_index_unique_bam.dedup_stats
#File SplitReads_cell_parser_hisat_summary = "?"
#File hicFiles = call_chromatin_contacts.chromatin_contact_stats
Expand All @@ -115,6 +114,8 @@ workflow WDLized_snm3C {
File unmapped_fastq_tar = Separate_unmapped_reads.unmapped_fastq_tar
File split_fq_tar = Split_unmapped_reads.split_fq_tar
File merge_sorted_bam_tar = Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name.merge_sorted_bam_tar
File name_sorted_bams = merge_original_and_split_bam_and_sort_all_reads_by_name_and_position.name_sorted_bam
File pos_sorted_bams = merge_original_and_split_bam_and_sort_all_reads_by_name_and_position.position_sorted_bam
File remove_overlap_read_parts_bam_tar = remove_overlap_read_parts.output_bam_tar
}
}
Expand Down Expand Up @@ -569,72 +570,101 @@ task Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name
}
task remove_overlap_read_parts {
input {
File bam
String docker = "us.gcr.io/broad-gotc-prod/m3c-yap-hisat:1.0.0-2.2.1"
Int disk_size = 80
Int mem_size = 20
}
command <<<
set -euo pipefail
# unzip bam file
tar -xf ~{bam}
rm ~{bam}
# create output dir
mkdir /cromwell_root/output_bams
# get bams
bams=($(ls | grep "sort.bam$"))
# loop through bams and run python script on each bam
# scatter instead of for loop to optimize
python3 <<CODE
from cemba_data.hisat3n import *
import os
bams="${bams[@]}"
for bam in bams.split(" "):
input {
File bam
String docker = "us.gcr.io/broad-gotc-prod/m3c-yap-hisat:1.0.0-2.2.1"
Int disk_size = 80
Int mem_size = 20
}
command <<<
set -euo pipefail
# unzip bam file
tar -xf ~{bam}
rm ~{bam}
# create output dir
mkdir /cromwell_root/output_bams
# get bams
bams=($(ls | grep "sort.bam$"))
# loop through bams and run python script on each bam
# scatter instead of for loop to optimize
python3 <<CODE
from cemba_data.hisat3n import *
import os
bams="${bams[@]}"
for bam in bams.split(" "):
name=".".join(bam.split(".")[:3])+".read_overlap.bam"
remove_overlap_read_parts(in_bam_path=os.path.join(os.path.sep, "cromwell_root", bam), out_bam_path=os.path.join(os.path.sep, "cromwell_root", "output_bams", name))
CODE
CODE
cd /cromwell_root/output_bams
cd /cromwell_root/output_bams
#tar up the merged bam files
tar -zcvf ../remove_overlap_read_parts.tar.gz *bam
#tar up the merged bam files
tar -zcvf ../remove_overlap_read_parts.tar.gz *bam
>>>
runtime {
docker: docker
disks: "local-disk ${disk_size} HDD"
cpu: 1
memory: "${mem_size} GiB"
}
output {
>>>
runtime {
docker: docker
disks: "local-disk ${disk_size} HDD"
cpu: 1
memory: "${mem_size} GiB"
}
output {
File output_bam_tar = "remove_overlap_read_parts.tar.gz"
}
}
#task merge_original_and_split_bam_and_sort_all_reads_by_name_and_position {
# input {
# File unique_bam
# File split_bam
# }
# command <<<
# >>>
# runtime {
# docker: "fill_in"
# disks: "local-disk ${disk_size} HDD"
# cpu: 1
# memory: "${mem_size} GiB"
# }
# output {
# File name_sorted_bam = ""
# File position_sorted_bam = ""
# }
#}
task merge_original_and_split_bam_and_sort_all_reads_by_name_and_position {
input {
File bam
File split_bam
String docker = "us.gcr.io/broad-gotc-prod/m3c-yap-hisat:1.0.0-2.2.1"
Int disk_size = 80
Int mem_size = 20
}
command <<<
set -euo pipefail
#unzip bam file
pwd
ls
tar -xf ~{bam}
tar -xf ~{split_bam}
rm ~{bam}
rm ~{split_bam}
pwd
ls
echo "samtools merge and sort"
# define lists of r1 and r2 fq files
UNIQUE_BAMS=($(ls | grep "\.hisat3n_dna.unique_aligned.bam"))
SPLIT_BAMS=($(ls | grep "\.hisat3n_dna.split_reads.read_overlap.bam"))
for file in "${UNIQUE_BAMS[@]}"; do
sample_id=$(basename "$file" ".hisat3n_dna.unique_aligned.bam")
samtools merge -f "${sample_id}.hisat3n_dna.all_reads.bam" "${sample_id}.hisat3n_dna.unique_aligned.bam" "${sample_id}.hisat3n_dna.split_reads.read_overlap.bam"
samtools sort -n -o "${sample_id}.hisat3n_dna.all_reads.name_sort.bam" "${sample_id}.hisat3n_dna.all_reads.bam"
samtools sort -O BAM -o "${sample_id}.hisat3n_dna.all_reads.pos_sort.bam" "${sample_id}.hisat3n_dna.all_reads.name_sort.bam"
done
echo "Tar files"
#tar up the merged bam files
tar -zcvf hisat3n_dna.all_reads.pos_sort.tar.gz *.hisat3n_dna.all_reads.pos_sort.bam
tar -zcvf hisat3n_dna.all_reads.name_sort.tar.gz *.hisat3n_dna.all_reads.name_sort.bam
ls
>>>
runtime {
docker: docker
disks: "local-disk ${disk_size} HDD"
cpu: 1
memory: "${mem_size} GiB"
}
output {
File name_sorted_bam = "hisat3n_dna.all_reads.name_sort.tar.gz"
File position_sorted_bam = "hisat3n_dna.all_reads.pos_sort.tar.gz"
}
}
#task call_chromatin_contacts {
# input {
Expand Down

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