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'main__run-with-toggle-label--active' : 'main__run-with-toggle-label--inactive'">Unix</div><div x-bind:class="!unix ? 'main__run-with-toggle-label--active' : 'main__run-with-toggle-label--inactive'">Windows</div></button></div><div class="main__run-with-content"><p class="main__run-with-content-text">sprocket run --entrypoint get_read_groups <span x-show="unix">data_structures/read_group.wdl</span><span x-show="!unix">data_structures\read_group.wdl</span> [INPUTS]...</p></div></div><div class="main__section"><h2 id="inputs" class="main__section-header">Inputs</h2><h3 id="required-inputs" class="main__section-subheader">Required Inputs</h3><div class="main__grid-container"><div class="main__grid-req-inputs-container"><div class="main__grid-header-cell">Name</div><div class="main__grid-header-cell">Type</div><div class="main__grid-header-cell">Description</div><div class="main__grid-header-separator"></div><div class="main__grid-row" x-data="{ description_expanded: false }"><div class="main__grid-cell"><code>bam</code></div><div class="main__grid-cell"><code>File</code></div><div class="main__grid-cell">Input BAM format file to get read groups from</div><div x-show="description_expanded" class="main__grid-full-width-cell">Input BAM format file to get read groups from</div></div></div></div><h3 id="other-inputs" class="main__section-subheader">Other Inputs</h3><div class="main__grid-container"><div class="main__grid-non-req-param-container"><div class="main__grid-header-cell">Name</div><div class="main__grid-header-cell">Type</div><div class="main__grid-header-cell">Default</div><div class="main__grid-header-cell">Description</div><div class="main__grid-header-separator"></div><div class="main__grid-row" x-data="{ description_expanded: false, expr_expanded: false }"><div class="main__grid-cell"><code>modify_disk_size_gb</code></div><div class="main__grid-cell"><code>Int</code></div><div class="main__grid-cell"><code>0</code></div><div class="main__grid-cell">Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.</div><div x-show="description_expanded" class="main__grid-full-width-cell">Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.</div><div x-show="expr_expanded" class="main__grid-full-width-cell"><sprocket-code language="wdl">0</sprocket-code></div></div></div></div></div><div class="main__section"><h2 id="outputs" class="main__section-header">Outputs</h2><div class="main__grid-container"><div class="main__grid-non-req-param-container"><div class="main__grid-header-cell">Name</div><div class="main__grid-header-cell">Type</div><div class="main__grid-header-cell">Expression</div><div class="main__grid-header-cell">Description</div><div class="main__grid-header-separator"></div><div class="main__grid-row" x-data="{ description_expanded: false, expr_expanded: false }"><div class="main__grid-cell"><code>read_groups</code></div><div class="main__grid-cell"><code>Array[ReadGroup]</code></div><div class="main__grid-cell"><code>read_json("read_groups.json")</code></div><div class="main__grid-cell">An array of ReadGroup structs containing read group information.</div><div x-show="description_expanded" class="main__grid-full-width-cell">An array of ReadGroup structs containing read group information.</div><div x-show="expr_expanded" class="main__grid-full-width-cell"><sprocket-code language="wdl">read_json("read_groups.json")</sprocket-code></div></div></div></div></div><div class="main__section"><h2 id="runtime" class="main__section-header">Default Runtime Attributes</h2><div class="main__grid-container"><div class="main__grid-runtime-container"><div class="main__grid-header-cell">Attribute</div><div class="main__grid-header-cell">Value</div><div class="main__grid-header-separator"></div><div class="main__grid-row"><div class="main__grid-cell"><code>memory</code></div><div class="main__grid-cell"><code>"4 GB"</code></div></div><div class="main__grid-row-separator"></div><div class="main__grid-row"><div class="main__grid-cell"><code>disks</code></div><div class="main__grid-cell"><code>"~{disk_size_gb} GB"</code></div></div><div class="main__grid-row-separator"></div><div class="main__grid-row"><div class="main__grid-cell"><code>container</code></div><div class="main__grid-cell"><code>"quay.io/biocontainers/pysam:0.22.0--py38h15b938a_1"</code></div></div><div class="main__grid-row-separator"></div><div class="main__grid-row"><div class="main__grid-cell"><code>maxRetries</code></div><div class="main__grid-cell"><code>1</code></div></div></div></div></div><div class="main__section"><h2 id="command" class="main__section-header">Command</h2><sprocket-code language="wdl" class="pt-8">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</sprocket-code></div></div></div></div><div class="layout__sidebar-right"><div class="right-sidebar__container"><div class="right-sidebar__header">ON THIS PAGE</div><a href="#inputs" class="right-sidebar__section-header">Inputs</a><div class="right-sidebar__section-items"><a href="#required-inputs" class="right-sidebar__section-item">Required Inputs</a></div><div class="right-sidebar__section-items"><a href="#other-inputs" class="right-sidebar__section-item">Other Inputs</a></div><a href="#outputs" class="right-sidebar__section-header">Outputs</a><a href="#runtime" class="right-sidebar__section-header">Runtime</a><a href="#command" class="right-sidebar__section-header">Command</a><div class="right-sidebar__back-to-top-container"><a href="#title" class="right-sidebar__back-to-top"><span class="right-sidebar__back-to-top-icon">↑</span><span class="right-sidebar__back-to-top-text">Back to top</span></a></div></div></div></div></body></html>