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" class="border border-slate-700 rounded-md h-8 flex items-center justify-center text-slate-300 text-lg w-8 cursor-pointer hover:border-slate-500">☀︎</button><div class="layout__breadcrumbs"><div class="layout__breadcrumb-container"><a class="layout__breadcrumb-clickable" href="../../index.html">docs</a><span> / </span><span class="layout__breadcrumb-inactive">data_structures</span><span> / </span><a href="index.html" class="layout__breadcrumb-clickable">read_group</a><span> / </span><span class="layout__breadcrumb-inactive">validate_read_group</span></div></div></div></div><div class="main__container"><span class="text-brand-violet-400">Task</span><h1 id="title" class="main__title"><code>validate_read_group</code></h1><div class="markdown-body mb-4">Validate a ReadGroup struct's fields are defined</div><div class="main__badge-container"><div class="main__badge"><span class="main__badge-text">WDL Version</span><div class="main__badge-inner"><span class="main__badge-inner-text">1.1</span></div></div></div><div x-data="{ unix: true }" class="main__run-with-container"><div class="main__run-with-label"><span class="main__run-with-label-text">RUN WITH</span><button x-on:click="unix = !unix" class="main__run-with-toggle"><div x-bind:class="unix ? '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 validate_read_group <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>read_group</code></div><div class="main__grid-cell"><code>ReadGroup</code></div><div class="main__grid-cell">ReadGroup struct to validate</div><div x-show="description_expanded" class="main__grid-full-width-cell">ReadGroup struct to validate</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>required_fields</code></div><div class="main__grid-cell"><code>Array[String]</code></div><div class="main__grid-cell"><code>[]</code></div><div class="main__grid-cell">Array of read group fields that must be defined. The ID field is always required and does not need to be specified.</div><div x-show="description_expanded" class="main__grid-full-width-cell">Array of read group fields that must be defined. The ID field is always required and does not need to be specified.</div><div x-show="expr_expanded" class="main__grid-full-width-cell"><sprocket-code language="wdl">[]</sprocket-code></div></div><div class="main__grid-row-separator"></div><div class="main__grid-row" x-data="{ description_expanded: false, expr_expanded: false }"><div class="main__grid-cell"><code>restrictive</code></div><div class="main__grid-cell"><code>Boolean</code></div><div class="main__grid-cell"><code>true</code></div><div class="main__grid-cell">If true, run a less permissive validation of field values. Otherwise, check against SAM spec-defined values.</div><div x-show="description_expanded" class="main__grid-full-width-cell">If true, run a less permissive validation of field values. Otherwise, check against SAM spec-defined values.</div><div x-show="expr_expanded" class="main__grid-full-width-cell"><sprocket-code language="wdl">true</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>check</code></div><div class="main__grid-cell"><code>String</code></div><div class="main__grid-cell"><code>"passed"</code></div><div class="main__grid-cell">Dummy output to indicate success and enable call-caching</div><div x-show="description_expanded" class="main__grid-full-width-cell">Dummy output to indicate success and enable call-caching</div><div x-show="expr_expanded" class="main__grid-full-width-cell"><sprocket-code language="wdl">"passed"</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>"10 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>"ghcr.io/stjudecloud/util:1.4.0"</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>0</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">error=0
if [[ ~{restrictive} == "true" ]]
then
if [[ ~{read_group.ID} =~ ^~{id_pattern}$ ]] \
|| [[ ~{read_group.ID} =~ ~{restrictive_pattern} ]]
then
>&2 echo "ID (~{read_group.ID}) must not match patterns:"
>&2 echo "'~{id_pattern}' or '~{restrictive_pattern}'"
error=1
fi
fi
if [[ ! "~{read_group.ID}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "ID must match pattern ~{sam_spec_pattern}"
error=1
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "SM") -eq 1 ]
then
if [ -z "~{read_group.SM}" ]
then
>&2 echo "SM is required"
error=1
fi
fi
if [ "~{defined(read_group.SM)}" == "true" ]
then
if [[ ~{restrictive} == "true" ]]
then
if [[ "~{read_group.SM}" =~ ^~{sample_pattern}$ ]] \
|| [[ "~{read_group.SM}" =~ ~{restrictive_pattern} ]]
then
>&2 echo "SM must not match patterns:"
>&2 echo "'~{sample_pattern}' or '~{restrictive_pattern}'"
error=1
fi
fi
if [[ ! "~{read_group.SM}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "SM must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "BC") -eq 1 ]
then
if [ -z "~{read_group.BC}" ]
then
>&2 echo "BC is required"
error=1
fi
fi
if [ "~{defined(read_group.BC)}" == "true" ]
then
if [[ ! "~{read_group.BC}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "BC must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "CN") -eq 1 ]
then
if [ -z "~{read_group.CN}" ]
then
>&2 echo "CN is required"
error=1
fi
fi
if [ "~{defined(read_group.CN)}" == "true" ]
then
if [[ ! "~{read_group.CN}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "CN must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "DS") -eq 1 ]
then
if [ -z "~{read_group.DS}" ]
then
>&2 echo "DS is required"
error=1
fi
fi
if [ "~{defined(read_group.DS)}" == "true" ]
then
if [[ ! "~{read_group.DS}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "DS must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "DT") -eq 1 ]
then
if [ -z "~{read_group.DT}" ]
then
>&2 echo "DT is required"
error=1
fi
fi
if [ "~{defined(read_group.DT)}" == "true" ]
then
if [[ ! "~{read_group.DT}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "DT must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "FO") -eq 1 ]
then
if [ -z "~{read_group.FO}" ]
then
>&2 echo "FO is required"
error=1
fi
fi
if [ "~{defined(read_group.FO)}" == "true" ]
then
if [[ ! "~{read_group.FO}" =~ ^\*|[ACMGRSVTWYHKDBN]+$ ]]
then
>&2 echo "FO must match pattern \*|[ACMGRSVTWYHKDBN]+"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "KS") -eq 1 ]
then
if [ -z "~{if defined(read_group.KS) then read_group.KS else ""}" ]
then
>&2 echo "KS is required"
error=1
fi
fi
if [ "~{defined(read_group.KS)}" == "true" ]
then
if [[ ! "~{read_group.KS}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "KS must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "LB") -eq 1 ]
then
if [ -z "~{read_group.LB}" ]
then
>&2 echo "LB is required"
error=1
fi
fi
if [ "~{defined(read_group.LB)}" == "true" ]
then
if [[ ! "~{read_group.LB}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "LB must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PG") -eq 1 ]
then
if [ -z "~{read_group.PG}" ]
then
>&2 echo "PG is required"
error=1
fi
fi
if [ "~{defined(read_group.PG)}" == "true" ]
then
if [[ ! "~{read_group.PG}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "PG must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PI") -eq 1 ]
then
if [ -z "~{read_group.PI}" ]
then
>&2 echo "PI is required"
error=1
fi
fi
if [ "~{defined(read_group.PI)}" == "true" ]
then
if [[ ! "~{read_group.PI}" =~ ^[0-9]+$ ]]
then
>&2 echo "PI must match pattern [0-9]+"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PL") -eq 1 ]
then
if [ -z "~{read_group.PL}" ]
then
>&2 echo "PL is required"
error=1
fi
fi
if [ "~{defined(read_group.PL)}" == "true" ]
then
if [[ ! "~{read_group.PL}" =~ ^~{sep("|", platforms)}$ ]]
then
>&2 echo "PL must match pattern ~{sep("|", platforms)}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PM") -eq 1 ]
then
if [ -z "~{read_group.PM}" ]
then
>&2 echo "PM is required"
error=1
fi
fi
if [ "~{defined(read_group.PM)}" == "true" ]
then
if [[ ! "~{read_group.PM}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "PM must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PU") -eq 1 ]
then
if [ -z "~{read_group.PU}" ]
then
>&2 echo "PU is required"
error=1
fi
fi
if [ "~{defined(read_group.PU)}" == "true" ]
then
if [[ ! "~{read_group.PU}" =~ ^~{sam_spec_pattern}$ ]]
then
>&2 echo "PU must match pattern ~{sam_spec_pattern}"
error=1
fi
fi
if [ $error -eq 1 ]
then
exit 1
fi</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>