`get_read_groups`

Gets read group information from a BAM file and writes it out as JSON which is converted to a WDL struct.

WDL Version

1.1

RUN WITH

sprocket run --name get_read_groups data_structures/read_group.wdldata_structures\read_group.wdl [INPUTS]...

Inputs

Required Inputs

Name

Type

Description

bam

File

Input BAM format file to get read groups from

Other Inputs

Name

Type

Default

Description

modify_disk_size_gb

Int

0

Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.

Outputs

Name

Type

Expression

Description

read_groups

Array[ReadGroup]

read_json("read_groups.json")

An array of ReadGroup structs containing read group information.

read_json("read_groups.json")

Default Runtime Attributes

Attribute

Value

memory

"4 GB"

disks

"~{disk_size_gb} GB"

container

"quay.io/biocontainers/pysam:0.22.0--py38h15b938a_1"

maxRetries

1

Command

set -euo pipefail BAM="~{bam}" OUTFILE="read_groups.json" python - <<END import os # lint-check: ignore import pysam # lint-check: ignore import json # lint-check: ignore sam = pysam.AlignmentFile(os.environ["BAM"], "rb") out_file = open(os.environ["OUTFILE"], "w") header = sam.header.to_dict()["RG"] modified_header = [] for read_group in sorted(header, key=lambda d: d['ID']): modified_header.append({k:v.upper() if k=='PL' else v for k,v in read_group.items()}) json.dump(modified_header, out_file) out_file.close() END