tag:github.com,2008:https://github.com/nf-core/raredisease/releases Release notes from raredisease 2025-02-24T13:56:36Z tag:github.com,2008:Repository/378880039/2.4.0 2025-02-24T13:58:38Z 2.4.0 - Vitalstatistix <h2>What's Changed</h2> <ul> <li>add markdup to multiqc by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2874179111" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/679" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/679/hovercard" href="https://github.com/nf-core/raredisease/pull/679">#679</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/2.3.0...2.4.0"><tt>2.3.0...2.4.0</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/2.3.0 2025-02-13T09:22:46Z 2.3.0 - Getafix <h2>What's Changed</h2> <ul> <li>Bumpversion 2.2.0-&gt;2.3.0dev by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2525031285" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/610" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/610/hovercard" href="https://github.com/nf-core/raredisease/pull/610">#610</a></li> <li>Add option to analyse only mitochondria by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2524743693" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/608" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/608/hovercard" href="https://github.com/nf-core/raredisease/pull/608">#608</a></li> <li>5% frequency threshold for mitochondrial clinical vcfs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2545405783" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/616" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/616/hovercard" href="https://github.com/nf-core/raredisease/pull/616">#616</a></li> <li>allow vep 112 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2545703566" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/617" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/617/hovercard" href="https://github.com/nf-core/raredisease/pull/617">#617</a></li> <li>Minor fixes by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2548077774" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/618" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/618/hovercard" href="https://github.com/nf-core/raredisease/pull/618">#618</a></li> <li>update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2556429311" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/619" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/619/hovercard" href="https://github.com/nf-core/raredisease/pull/619">#619</a></li> <li>Change output file prefix for upd and chromograph by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2558982473" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/620" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/620/hovercard" href="https://github.com/nf-core/raredisease/pull/620">#620</a></li> <li>Invoke rhocallviz subworkflow only once per sample. by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2559014357" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/621" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/621/hovercard" href="https://github.com/nf-core/raredisease/pull/621">#621</a></li> <li>Update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2561874163" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/623" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/623/hovercard" href="https://github.com/nf-core/raredisease/pull/623">#623</a></li> <li>Fix channel declaration error in the cadd subworkflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2565737033" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/624" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/624/hovercard" href="https://github.com/nf-core/raredisease/pull/624">#624</a></li> <li>Update genmod and multiqc by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2569546214" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/625" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/625/hovercard" href="https://github.com/nf-core/raredisease/pull/625">#625</a></li> <li>template update 3.0.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2578227441" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/629" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/629/hovercard" href="https://github.com/nf-core/raredisease/pull/629">#629</a></li> <li>Important! Template update for nf-core/tools v3.0.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2575687860" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/628" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/628/hovercard" href="https://github.com/nf-core/raredisease/pull/628">#628</a></li> <li>Important! Template update for nf-core/tools v3.0.2 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2581361040" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/630" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/630/hovercard" href="https://github.com/nf-core/raredisease/pull/630">#630</a></li> <li>ensure string comparison by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2584983384" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/632" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/632/hovercard" href="https://github.com/nf-core/raredisease/pull/632">#632</a></li> <li>add bait regions to deepvariant for WES by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2586301847" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/633" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/633/hovercard" href="https://github.com/nf-core/raredisease/pull/633">#633</a></li> <li>Merge germlinecnvcaller output by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2594680718" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/635" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/635/hovercard" href="https://github.com/nf-core/raredisease/pull/635">#635</a></li> <li>Raredisease: Add fastp output to multiqc by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/peterpru/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/peterpru">@peterpru</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2597405891" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/637" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/637/hovercard" href="https://github.com/nf-core/raredisease/pull/637">#637</a></li> <li>Fix fastqc samplenames in multiqc report by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2602663519" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/638" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/638/hovercard" href="https://github.com/nf-core/raredisease/pull/638">#638</a></li> <li>Vep update to 113 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2602743776" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/639" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/639/hovercard" href="https://github.com/nf-core/raredisease/pull/639">#639</a></li> <li>Use target bed files as regions instead of bait intervals for SNV calling in WES samples by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2596779204" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/636" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/636/hovercard" href="https://github.com/nf-core/raredisease/pull/636">#636</a></li> <li>Upd fix by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2624581421" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/643" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/643/hovercard" href="https://github.com/nf-core/raredisease/pull/643">#643</a></li> <li>Update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2648503086" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/646" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/646/hovercard" href="https://github.com/nf-core/raredisease/pull/646">#646</a></li> <li>Add option to restrict analysis to specific contigs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2643575600" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/644" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/644/hovercard" href="https://github.com/nf-core/raredisease/pull/644">#644</a></li> <li>add fastp and ngsbits to multiqc input by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/peterpru/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/peterpru">@peterpru</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2649325643" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/647" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/647/hovercard" href="https://github.com/nf-core/raredisease/pull/647">#647</a></li> <li>Fix tests by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2680074224" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/648" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/648/hovercard" href="https://github.com/nf-core/raredisease/pull/648">#648</a></li> <li>patch vep 110 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2690317631" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/649" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/649/hovercard" href="https://github.com/nf-core/raredisease/pull/649">#649</a></li> <li>Sync v3.1.1 of nf-core template by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2772503647" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/655" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/655/hovercard" href="https://github.com/nf-core/raredisease/pull/655">#655</a></li> <li>Important! Template update for nf-core/tools v3.1.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2752713359" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/654" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/654/hovercard" href="https://github.com/nf-core/raredisease/pull/654">#654</a></li> <li>Remove suffixes sample name in repeat call vcfs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2773092932" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/657" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/657/hovercard" href="https://github.com/nf-core/raredisease/pull/657">#657</a></li> <li>Update module MultiQC to version 1.26 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/peterpru/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/peterpru">@peterpru</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2777956253" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/660" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/660/hovercard" href="https://github.com/nf-core/raredisease/pull/660">#660</a></li> <li>padding bed file by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2775760123" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/658" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/658/hovercard" href="https://github.com/nf-core/raredisease/pull/658">#658</a></li> <li>Fix sex by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2777836672" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/659" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/659/hovercard" href="https://github.com/nf-core/raredisease/pull/659">#659</a></li> <li>Pre release PR1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2789504204" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/664" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/664/hovercard" href="https://github.com/nf-core/raredisease/pull/664">#664</a></li> <li>set meta.id for some input files by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2780481795" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/661" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/661/hovercard" href="https://github.com/nf-core/raredisease/pull/661">#661</a></li> <li>Add haplocheck to multiqc by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/fevac/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/fevac">@fevac</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2787407543" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/662" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/662/hovercard" href="https://github.com/nf-core/raredisease/pull/662">#662</a></li> <li>Pre release PR2 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2795431011" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/665" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/665/hovercard" href="https://github.com/nf-core/raredisease/pull/665">#665</a></li> <li>Fix download tests by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2798469467" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/667" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/667/hovercard" href="https://github.com/nf-core/raredisease/pull/667">#667</a></li> <li>Important! Template update for nf-core/tools v3.1.2 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2799432817" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/668" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/668/hovercard" href="https://github.com/nf-core/raredisease/pull/668">#668</a></li> <li>Review suggestions on v2.3.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2803980950" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/669" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/669/hovercard" href="https://github.com/nf-core/raredisease/pull/669">#669</a></li> <li>Template update v320 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2813636552" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/671" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/671/hovercard" href="https://github.com/nf-core/raredisease/pull/671">#671</a></li> <li>Important! Template update for nf-core/tools v3.2.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2813326084" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/670" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/670/hovercard" href="https://github.com/nf-core/raredisease/pull/670">#670</a></li> <li>update haplogrep3 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2816084941" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/672" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/672/hovercard" href="https://github.com/nf-core/raredisease/pull/672">#672</a></li> <li>Keep only SVs that PASS the filter by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2817930333" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/673" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/673/hovercard" href="https://github.com/nf-core/raredisease/pull/673">#673</a></li> <li>Update versions by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2823724907" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/674" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/674/hovercard" href="https://github.com/nf-core/raredisease/pull/674">#674</a></li> <li>Add option to skip haplogrep3 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2830198337" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/675" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/675/hovercard" href="https://github.com/nf-core/raredisease/pull/675">#675</a></li> <li>Release v2.3.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2795912016" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/666" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/666/hovercard" href="https://github.com/nf-core/raredisease/pull/666">#666</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/fevac/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/fevac">@fevac</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2787407543" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/662" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/662/hovercard" href="https://github.com/nf-core/raredisease/pull/662">#662</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/2.2.0...2.3.0"><tt>2.2.0...2.3.0</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/2.2.0 2024-09-13T14:44:59Z 2.2.0 - Dogmatix <h2>What's Changed</h2> <ul> <li>typo by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/EmelineFavreau/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/EmelineFavreau">@EmelineFavreau</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2330712170" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/562" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/562/hovercard" href="https://github.com/nf-core/raredisease/pull/562">#562</a></li> <li>adds missinf citations for bwameme by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2336322116" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/563" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/563/hovercard" href="https://github.com/nf-core/raredisease/pull/563">#563</a></li> <li>Few fixes by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2364864093" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/570" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/570/hovercard" href="https://github.com/nf-core/raredisease/pull/570">#570</a></li> <li>Add parameters to skip snv calling and repeat analysis by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2369677533" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/571" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/571/hovercard" href="https://github.com/nf-core/raredisease/pull/571">#571</a></li> <li>Add a new paramter to skip sv calling by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2370143870" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/572" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/572/hovercard" href="https://github.com/nf-core/raredisease/pull/572">#572</a></li> <li>Turn off workflows irrelevant for WES analysis by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2370268399" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/573" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/573/hovercard" href="https://github.com/nf-core/raredisease/pull/573">#573</a></li> <li>Refactor by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2370452024" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/574" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/574/hovercard" href="https://github.com/nf-core/raredisease/pull/574">#574</a></li> <li>update peddy module by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2375100503" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/576" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/576/hovercard" href="https://github.com/nf-core/raredisease/pull/576">#576</a></li> <li>Refactor citations by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2376172058" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/577" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/577/hovercard" href="https://github.com/nf-core/raredisease/pull/577">#577</a></li> <li>Fix WES error by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2383453679" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/578" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/578/hovercard" href="https://github.com/nf-core/raredisease/pull/578">#578</a></li> <li>Bcftools roh logic update by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2386115305" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/579" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/579/hovercard" href="https://github.com/nf-core/raredisease/pull/579">#579</a></li> <li>adds channels to meme mt align by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2390479321" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/582" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/582/hovercard" href="https://github.com/nf-core/raredisease/pull/582">#582</a></li> <li>fix: added publishDir mode in raredisease.config by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/irliampa/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/irliampa">@irliampa</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2429978810" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/584" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/584/hovercard" href="https://github.com/nf-core/raredisease/pull/584">#584</a></li> <li>Reorder SNV annotation subworkflow to improve performance by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2445031618" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/585" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/585/hovercard" href="https://github.com/nf-core/raredisease/pull/585">#585</a></li> <li>SV calling error in WES samples by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2453745855" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/586" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/586/hovercard" href="https://github.com/nf-core/raredisease/pull/586">#586</a></li> <li>Deepvariant update v1.6.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2455048499" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/587" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/587/hovercard" href="https://github.com/nf-core/raredisease/pull/587">#587</a></li> <li>Add an option to pass extra resources to vcfanno by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2457251654" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/588" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/588/hovercard" href="https://github.com/nf-core/raredisease/pull/588">#588</a></li> <li>Add feature to pass vcf.gz files as an additional resource for vcfanno by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2458030637" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/589" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/589/hovercard" href="https://github.com/nf-core/raredisease/pull/589">#589</a></li> <li>makes 0 an allowed value for sex by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2465319541" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/595" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/595/hovercard" href="https://github.com/nf-core/raredisease/pull/595">#595</a></li> <li>Update docs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2463533699" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/594" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/594/hovercard" href="https://github.com/nf-core/raredisease/pull/594">#594</a></li> <li>Change lane type from number to string by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2465702902" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/597" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/597/hovercard" href="https://github.com/nf-core/raredisease/pull/597">#597</a></li> <li>Add option to supply bed file with PAR regions &amp; enable haploid analysis for males by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2466045518" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/598" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/598/hovercard" href="https://github.com/nf-core/raredisease/pull/598">#598</a></li> <li>bwamem2 for mt by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2473529264" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/600" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/600/hovercard" href="https://github.com/nf-core/raredisease/pull/600">#600</a></li> <li>Updating Sentieon DNAscope ml-model by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2475326912" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/601" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/601/hovercard" href="https://github.com/nf-core/raredisease/pull/601">#601</a></li> <li>Resolve issues that cropped up when aligner and mt_aligner were different by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2489030835" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/605" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/605/hovercard" href="https://github.com/nf-core/raredisease/pull/605">#605</a></li> <li>Add option to generate csi index for managed variants by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2496754086" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/606" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/606/hovercard" href="https://github.com/nf-core/raredisease/pull/606">#606</a></li> <li>Change platform description and update vcf2cytosure conditional by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2519370566" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/607" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/607/hovercard" href="https://github.com/nf-core/raredisease/pull/607">#607</a></li> <li>Updatevep from v110-112 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2524763564" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/609" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/609/hovercard" href="https://github.com/nf-core/raredisease/pull/609">#609</a></li> <li>Release 2.2.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2388562515" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/580" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/580/hovercard" href="https://github.com/nf-core/raredisease/pull/580">#580</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/EmelineFavreau/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/EmelineFavreau">@EmelineFavreau</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2330712170" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/562" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/562/hovercard" href="https://github.com/nf-core/raredisease/pull/562">#562</a></li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/irliampa/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/irliampa">@irliampa</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2429978810" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/584" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/584/hovercard" href="https://github.com/nf-core/raredisease/pull/584">#584</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/2.1.0...2.2.0"><tt>2.1.0...2.2.0</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/2.1.0 2024-05-29T10:28:20Z 2.1.0 - Obelix <h2>What's Changed</h2> <ul> <li>Bumpversion 2.1.0dev by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2191755033" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/533" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/533/hovercard" href="https://github.com/nf-core/raredisease/pull/533">#533</a></li> <li>Update changelog by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2192307239" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/534" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/534/hovercard" href="https://github.com/nf-core/raredisease/pull/534">#534</a></li> <li>adding explicit temps by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2268593687" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/541" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/541/hovercard" href="https://github.com/nf-core/raredisease/pull/541">#541</a></li> <li>Template update v2.14.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2295138618" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/548" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/548/hovercard" href="https://github.com/nf-core/raredisease/pull/548">#548</a></li> <li>Important! Template update for nf-core/tools v2.14.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2287513660" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/547" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/547/hovercard" href="https://github.com/nf-core/raredisease/pull/547">#547</a></li> <li>Include "other" variants for CADD to analyse multallelic indels by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/fa2k/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/fa2k">@fa2k</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2281155311" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/545" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/545/hovercard" href="https://github.com/nf-core/raredisease/pull/545">#545</a></li> <li>Refactoring + other issues with cadd and samtools merge by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2245836824" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/538" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/538/hovercard" href="https://github.com/nf-core/raredisease/pull/538">#538</a></li> <li>Bwafallback by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2302442087" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/551" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/551/hovercard" href="https://github.com/nf-core/raredisease/pull/551">#551</a></li> <li>changed valid values for the sex variable by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/sima-r/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/sima-r">@sima-r</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2299724309" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/550" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/550/hovercard" href="https://github.com/nf-core/raredisease/pull/550">#550</a></li> <li>Skip mitochondrial analysis for WES by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2303277708" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/552" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/552/hovercard" href="https://github.com/nf-core/raredisease/pull/552">#552</a></li> <li>Add bwameme by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2304641416" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/553" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/553/hovercard" href="https://github.com/nf-core/raredisease/pull/553">#553</a></li> <li>Fix join issues in ME calling subworkflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2312758135" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/556" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/556/hovercard" href="https://github.com/nf-core/raredisease/pull/556">#556</a></li> <li>Resolve warnings by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2315263570" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/557" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/557/hovercard" href="https://github.com/nf-core/raredisease/pull/557">#557</a></li> <li>updating meta.sex type check by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2318635818" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/559" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/559/hovercard" href="https://github.com/nf-core/raredisease/pull/559">#559</a></li> <li>update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2315355320" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/558" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/558/hovercard" href="https://github.com/nf-core/raredisease/pull/558">#558</a></li> <li>refactor by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2320816350" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/561" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/561/hovercard" href="https://github.com/nf-core/raredisease/pull/561">#561</a></li> <li>Release 2.1.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2312666622" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/555" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/555/hovercard" href="https://github.com/nf-core/raredisease/pull/555">#555</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/2.0.1...2.1.0"><tt>2.0.1...2.1.0</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/2.0.1 2024-03-25T12:56:58Z 2.0.1 - Asterix (patch) <h2>What's Changed</h2> <ul> <li>Address the right emit channel from the germlinecnvcaller module (<code>cohortcalls</code> instead of <code>calls</code>) - by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2205449189" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/536" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/536/hovercard" href="https://github.com/nf-core/raredisease/pull/536">#536</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/2.0.0...2.0.1"><tt>2.0.0...2.0.1</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/2.0.0 2024-03-18T09:52:08Z 2.0.0 - Asterix <h2>What's Changed</h2> <ul> <li>bumpversion to 1.2.0dev by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1815835610" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/384" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/384/hovercard" href="https://github.com/nf-core/raredisease/pull/384">#384</a></li> <li>Updating tiddit to v3.6.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1817129930" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/385" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/385/hovercard" href="https://github.com/nf-core/raredisease/pull/385">#385</a></li> <li>Sync dev to latest master with changes from patch release 1.1.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1822408815" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/390" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/390/hovercard" href="https://github.com/nf-core/raredisease/pull/390">#390</a></li> <li>switch to nf-validation for parameter and samplesheet validation by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1819043026" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/386" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/386/hovercard" href="https://github.com/nf-core/raredisease/pull/386">#386</a></li> <li>Correct GATK4 container spec by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/adamrtalbot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/adamrtalbot">@adamrtalbot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1824058139" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/391" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/391/hovercard" href="https://github.com/nf-core/raredisease/pull/391">#391</a></li> <li>Make cram prefix same as the default markduplicates prefix by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1829227010" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/392" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/392/hovercard" href="https://github.com/nf-core/raredisease/pull/392">#392</a></li> <li>Update documentation by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1831434527" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/394" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/394/hovercard" href="https://github.com/nf-core/raredisease/pull/394">#394</a></li> <li>Add constraints to block the pipeline from running CollectWgsMetrics on WES samples by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1833398205" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/396" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/396/hovercard" href="https://github.com/nf-core/raredisease/pull/396">#396</a></li> <li>Make target bed file optional for WGS mode by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1831645674" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/395" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/395/hovercard" href="https://github.com/nf-core/raredisease/pull/395">#395</a></li> <li>Update sentieon bwamemindex by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1841258622" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/397" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/397/hovercard" href="https://github.com/nf-core/raredisease/pull/397">#397</a></li> <li>sort ranked SVs before indexing by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1831389626" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/393" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/393/hovercard" href="https://github.com/nf-core/raredisease/pull/393">#393</a></li> <li>Installing and calling nf-core/modules version of sentieon/bwamem by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1843416946" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/398" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/398/hovercard" href="https://github.com/nf-core/raredisease/pull/398">#398</a></li> <li>Replace local version of SENTIEON_READWRITER with nf-core version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1849364838" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/399" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/399/hovercard" href="https://github.com/nf-core/raredisease/pull/399">#399</a></li> <li>Replace local version of SENTIEON_DATAMETRICS with nf-core version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1849609922" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/400" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/400/hovercard" href="https://github.com/nf-core/raredisease/pull/400">#400</a></li> <li>Replace local version of sentieon-locuscollector and sentieon-dedup by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1849696270" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/401" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/401/hovercard" href="https://github.com/nf-core/raredisease/pull/401">#401</a></li> <li>Remove sentieon BQSR by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1850136082" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/402" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/402/hovercard" href="https://github.com/nf-core/raredisease/pull/402">#402</a></li> <li>Replace local version of SENTIEON_DNAMODELAPPLY with nf-core version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1851043462" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/403" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/403/hovercard" href="https://github.com/nf-core/raredisease/pull/403">#403</a></li> <li>Replace local version of SENTIEON_WGSMETRICS with nf-core version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1851324861" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/404" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/404/hovercard" href="https://github.com/nf-core/raredisease/pull/404">#404</a></li> <li>Add documentation for running without Internet access by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/fa2k/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/fa2k">@fa2k</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1821899624" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/389" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/389/hovercard" href="https://github.com/nf-core/raredisease/pull/389">#389</a></li> <li>Add sentieon/dnascope from nf-core/modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1854600574" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/406" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/406/hovercard" href="https://github.com/nf-core/raredisease/pull/406">#406</a></li> <li>Set "0" a default for missing maternal and paternal id in ped file by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1856844434" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/411" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/411/hovercard" href="https://github.com/nf-core/raredisease/pull/411">#411</a></li> <li>Update modules to their latest nf-core version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1857670662" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/412" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/412/hovercard" href="https://github.com/nf-core/raredisease/pull/412">#412</a></li> <li>Add skip_vep_filter parameter by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1863389451" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/416" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/416/hovercard" href="https://github.com/nf-core/raredisease/pull/416">#416</a></li> <li>Remove duplicate entries from probands and upd_children in meta by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1879661345" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/420" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/420/hovercard" href="https://github.com/nf-core/raredisease/pull/420">#420</a></li> <li>Fixes vep starting as many instances as the square of the number of scatters by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1880123863" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/421" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/421/hovercard" href="https://github.com/nf-core/raredisease/pull/421">#421</a></li> <li>Update dnascope-module by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1882147954" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/422" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/422/hovercard" href="https://github.com/nf-core/raredisease/pull/422">#422</a></li> <li>Add a new sample field to meta by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1894761980" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/425" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/425/hovercard" href="https://github.com/nf-core/raredisease/pull/425">#425</a></li> <li>Refactor mitochondrial analysis workflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1875972542" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/419" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/419/hovercard" href="https://github.com/nf-core/raredisease/pull/419">#419</a></li> <li>Template updates v2.10 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1917351741" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/431" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/431/hovercard" href="https://github.com/nf-core/raredisease/pull/431">#431</a></li> <li>add metromap with core elements by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1905036714" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/428" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/428/hovercard" href="https://github.com/nf-core/raredisease/pull/428">#428</a></li> <li>Add logo+metromap for both light and dark themes by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1924103046" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/432" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/432/hovercard" href="https://github.com/nf-core/raredisease/pull/432">#432</a></li> <li>add skip_qualimap and skip_eklipse parameters by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1947636115" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/436" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/436/hovercard" href="https://github.com/nf-core/raredisease/pull/436">#436</a></li> <li>fix warnings and clean up terminal logs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1947475996" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/435" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/435/hovercard" href="https://github.com/nf-core/raredisease/pull/435">#435</a></li> <li>skip haplocheck and fastqc [skip ci] by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1963423115" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/438" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/438/hovercard" href="https://github.com/nf-core/raredisease/pull/438">#438</a></li> <li>Add cnvnator subworkflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1945644888" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/434" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/434/hovercard" href="https://github.com/nf-core/raredisease/pull/434">#434</a></li> <li>addressing <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1911003023" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/429" data-hovercard-type="issue" data-hovercard-url="/nf-core/raredisease/issues/429/hovercard" href="https://github.com/nf-core/raredisease/issues/429">#429</a> by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1992689862" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/445" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/445/hovercard" href="https://github.com/nf-core/raredisease/pull/445">#445</a></li> <li>Document which variantcatalogs to use by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1992352070" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/443" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/443/hovercard" href="https://github.com/nf-core/raredisease/pull/443">#443</a></li> <li>Update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2007940925" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/449" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/449/hovercard" href="https://github.com/nf-core/raredisease/pull/449">#449</a></li> <li>Fix mem qualifier by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2020446252" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/451" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/451/hovercard" href="https://github.com/nf-core/raredisease/pull/451">#451</a></li> <li>Add sex check by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Lucpen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Lucpen">@Lucpen</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2040601657" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/453" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/453/hovercard" href="https://github.com/nf-core/raredisease/pull/453">#453</a></li> <li>Fix two instances of wrong process name passed to <code>ch_versions.mix()</code> when running in sentieon mode by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/alkc/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/alkc">@alkc</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2043923304" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/454" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/454/hovercard" href="https://github.com/nf-core/raredisease/pull/454">#454</a></li> <li>feat add fastp by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Lucpen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Lucpen">@Lucpen</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2046896933" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/457" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/457/hovercard" href="https://github.com/nf-core/raredisease/pull/457">#457</a></li> <li>Vcf2cytosure by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2046856888" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/456" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/456/hovercard" href="https://github.com/nf-core/raredisease/pull/456">#456</a></li> <li>Nf core template update by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2050728023" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/461" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/461/hovercard" href="https://github.com/nf-core/raredisease/pull/461">#461</a></li> <li>Important! Template update for nf-core/tools v2.11.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2050851552" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/463" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/463/hovercard" href="https://github.com/nf-core/raredisease/pull/463">#463</a></li> <li>feat added specific values for some samplesheet params by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Lucpen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Lucpen">@Lucpen</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2050477109" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/459" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/459/hovercard" href="https://github.com/nf-core/raredisease/pull/459">#459</a></li> <li>GATK CNVCaller fixes by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Jakob37/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Jakob37">@Jakob37</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2073806929" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/472" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/472/hovercard" href="https://github.com/nf-core/raredisease/pull/472">#472</a></li> <li>Updating vcf2cytosure and tiddit cov by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2072768607" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/470" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/470/hovercard" href="https://github.com/nf-core/raredisease/pull/470">#470</a></li> <li>Add found_in tag to vcf by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2073588746" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/471" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/471/hovercard" href="https://github.com/nf-core/raredisease/pull/471">#471</a></li> <li>Change hardcoded platform value to params.platform in modules/align_MT.config by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/alkc/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/alkc">@alkc</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2076170661" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/475" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/475/hovercard" href="https://github.com/nf-core/raredisease/pull/475">#475</a></li> <li>adds schema for svdb query inputs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2076648249" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/476" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/476/hovercard" href="https://github.com/nf-core/raredisease/pull/476">#476</a></li> <li>Add bwa mem by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2075887670" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/474" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/474/hovercard" href="https://github.com/nf-core/raredisease/pull/474">#474</a></li> <li>Fix for getting chr sizes when fai is given by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2079244201" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/479" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/479/hovercard" href="https://github.com/nf-core/raredisease/pull/479">#479</a></li> <li>Add mobile element calling to raredisease by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/peterpru/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/peterpru">@peterpru</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1978989864" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/440" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/440/hovercard" href="https://github.com/nf-core/raredisease/pull/440">#440</a></li> <li>fix number of me channels by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2083877347" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/481" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/481/hovercard" href="https://github.com/nf-core/raredisease/pull/481">#481</a></li> <li>Subworkflow for mobile element annotation by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2088150556" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/483" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/483/hovercard" href="https://github.com/nf-core/raredisease/pull/483">#483</a></li> <li>Vep update by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2084660830" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/482" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/482/hovercard" href="https://github.com/nf-core/raredisease/pull/482">#482</a></li> <li>Add rtgtools by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2093449599" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/484" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/484/hovercard" href="https://github.com/nf-core/raredisease/pull/484">#484</a></li> <li>Update RG generation string by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2099890160" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/487" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/487/hovercard" href="https://github.com/nf-core/raredisease/pull/487">#487</a></li> <li>refactoring clinical research split by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2093635137" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/485" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/485/hovercard" href="https://github.com/nf-core/raredisease/pull/485">#485</a></li> <li>Update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2100113195" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/488" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/488/hovercard" href="https://github.com/nf-core/raredisease/pull/488">#488</a></li> <li>Template update to 2.12 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2107277976" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/501" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/501/hovercard" href="https://github.com/nf-core/raredisease/pull/501">#501</a></li> <li>Important! Template update for nf-core/tools v2.12 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2105814045" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/499" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/499/hovercard" href="https://github.com/nf-core/raredisease/pull/499">#499</a></li> <li>Vep pli update by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Lucpen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Lucpen">@Lucpen</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2105460974" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/491" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/491/hovercard" href="https://github.com/nf-core/raredisease/pull/491">#491</a></li> <li>Refactor code and configs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2105425325" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/490" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/490/hovercard" href="https://github.com/nf-core/raredisease/pull/490">#490</a></li> <li>fix input channel for vcf2cytosure subworkflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2105903416" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/500" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/500/hovercard" href="https://github.com/nf-core/raredisease/pull/500">#500</a></li> <li>cnvnator patch by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2109605013" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/503" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/503/hovercard" href="https://github.com/nf-core/raredisease/pull/503">#503</a></li> <li>update expansionhunter by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2108365703" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/502" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/502/hovercard" href="https://github.com/nf-core/raredisease/pull/502">#502</a></li> <li>minor edit to output documentation by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2110411182" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/504" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/504/hovercard" href="https://github.com/nf-core/raredisease/pull/504">#504</a></li> <li>Added a local module to generate bed files with variant caller annotations by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2111164565" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/505" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/505/hovercard" href="https://github.com/nf-core/raredisease/pull/505">#505</a></li> <li>Update modules by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2112434933" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/506" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/506/hovercard" href="https://github.com/nf-core/raredisease/pull/506">#506</a></li> <li>Chromograph viz by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2112888766" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/507" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/507/hovercard" href="https://github.com/nf-core/raredisease/pull/507">#507</a></li> <li>Add subsample mt by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2114553871" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/508" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/508/hovercard" href="https://github.com/nf-core/raredisease/pull/508">#508</a></li> <li>Add parameter to supply variant consequence files by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2115790000" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/510" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/510/hovercard" href="https://github.com/nf-core/raredisease/pull/510">#510</a></li> <li>add new parameter to supply a bed like file for filtering vep results by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2116834046" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/511" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/511/hovercard" href="https://github.com/nf-core/raredisease/pull/511">#511</a></li> <li>Add rhocall viz by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2120752819" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/512" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/512/hovercard" href="https://github.com/nf-core/raredisease/pull/512">#512</a></li> <li>updating gens subworkflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/jemten/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/jemten">@jemten</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2132025115" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/515" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/515/hovercard" href="https://github.com/nf-core/raredisease/pull/515">#515</a></li> <li>Rename outputs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2134650035" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/516" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/516/hovercard" href="https://github.com/nf-core/raredisease/pull/516">#516</a></li> <li>Template update v 2.13 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2145468021" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/518" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/518/hovercard" href="https://github.com/nf-core/raredisease/pull/518">#518</a></li> <li>Important! Template update for nf-core/tools v2.13 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2144649266" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/517" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/517/hovercard" href="https://github.com/nf-core/raredisease/pull/517">#517</a></li> <li>Normalize repeat expansions by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2160793250" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/524" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/524/hovercard" href="https://github.com/nf-core/raredisease/pull/524">#524</a></li> <li>chromograph autozyg by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2160644806" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/523" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/523/hovercard" href="https://github.com/nf-core/raredisease/pull/523">#523</a></li> <li>Fix samplenames in smncopynumbercaller by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2160001464" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/522" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/522/hovercard" href="https://github.com/nf-core/raredisease/pull/522">#522</a></li> <li>Important! Template update for nf-core/tools v2.13.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/nf-core-bot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/nf-core-bot">@nf-core-bot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2163139187" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/525" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/525/hovercard" href="https://github.com/nf-core/raredisease/pull/525">#525</a></li> <li>Add option to annotate vcf2cytosure file with different(customer) ids by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2159717983" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/521" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/521/hovercard" href="https://github.com/nf-core/raredisease/pull/521">#521</a></li> <li>modules update by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2166550885" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/526" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/526/hovercard" href="https://github.com/nf-core/raredisease/pull/526">#526</a></li> <li>Release prep v2.0.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2168927244" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/527" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/527/hovercard" href="https://github.com/nf-core/raredisease/pull/527">#527</a></li> <li>Test download cleanup by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2169565986" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/529" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/529/hovercard" href="https://github.com/nf-core/raredisease/pull/529">#529</a></li> <li>fix: parameters not resolving properly when igenomes are used by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2178552857" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/530" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/530/hovercard" href="https://github.com/nf-core/raredisease/pull/530">#530</a></li> <li>Release 2.0.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2169186155" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/528" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/528/hovercard" href="https://github.com/nf-core/raredisease/pull/528">#528</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/alkc/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/alkc">@alkc</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2043923304" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/454" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/454/hovercard" href="https://github.com/nf-core/raredisease/pull/454">#454</a></li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Jakob37/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Jakob37">@Jakob37</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2073806929" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/472" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/472/hovercard" href="https://github.com/nf-core/raredisease/pull/472">#472</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/1.1.1...2.0.0"><tt>1.1.1...2.0.0</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/1.1.1 2023-07-26T08:56:58Z 1.1.1 - Abu (patch) <h2>What's Changed</h2> <ul> <li>Patch release v1.1.1 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1820650716" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/388" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/388/hovercard" href="https://github.com/nf-core/raredisease/pull/388">#388</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/1.1.0...1.1.1"><tt>1.1.0...1.1.1</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/1.1.0 2023-07-21T10:22:06Z 1.1.0 - Abu <h2>What's Changed</h2> <ul> <li>Annotate small indels with CADD scores by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1651912798" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/325" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/325/hovercard" href="https://github.com/nf-core/raredisease/pull/325">#325</a></li> <li>convert bam to cram by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1697607613" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/340" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/340/hovercard" href="https://github.com/nf-core/raredisease/pull/340">#340</a></li> <li>Add shiftfasta by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1727196480" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/354" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/354/hovercard" href="https://github.com/nf-core/raredisease/pull/354">#354</a></li> <li>feat added MT deletion script by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Lucpen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Lucpen">@Lucpen</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1722139055" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/349" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/349/hovercard" href="https://github.com/nf-core/raredisease/pull/349">#349</a></li> <li>Adding upd by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/hrydbeck/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/hrydbeck">@hrydbeck</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1767715173" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/364" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/364/hovercard" href="https://github.com/nf-core/raredisease/pull/364">#364</a></li> <li>Add ek by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/Lucpen/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/Lucpen">@Lucpen</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1774167398" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/365" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/365/hovercard" href="https://github.com/nf-core/raredisease/pull/365">#365</a></li> <li>add chromograph by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1774907604" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/366" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/366/hovercard" href="https://github.com/nf-core/raredisease/pull/366">#366</a></li> <li>Update to template 2.9 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1788159886" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/372" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/372/hovercard" href="https://github.com/nf-core/raredisease/pull/372">#372</a></li> <li>Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1780781832" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/368" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/368/hovercard" href="https://github.com/nf-core/raredisease/pull/368">#368</a></li> <li>added check for case id by @EmmaCAndersson in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1731809217" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/357" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/357/hovercard" href="https://github.com/nf-core/raredisease/pull/357">#357</a></li> <li>Gatkcnvcaller by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1745870831" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/362" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/362/hovercard" href="https://github.com/nf-core/raredisease/pull/362">#362</a></li> <li>Update schema, output.md, and remove unused parameters by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1793545475" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/373" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/373/hovercard" href="https://github.com/nf-core/raredisease/pull/373">#373</a></li> <li>update eklipse by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/ramprasadn/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/ramprasadn">@ramprasadn</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1793576826" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/374" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/374/hovercard" href="https://github.com/nf-core/raredisease/pull/374">#374</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/adamrtalbot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/adamrtalbot">@adamrtalbot</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1737818761" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/360" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/360/hovercard" href="https://github.com/nf-core/raredisease/pull/360">#360</a></li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/hrydbeck/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/hrydbeck">@hrydbeck</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1767715173" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/364" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/364/hovercard" href="https://github.com/nf-core/raredisease/pull/364">#364</a></li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/asp8200/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/asp8200">@asp8200</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1780781832" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/368" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/368/hovercard" href="https://github.com/nf-core/raredisease/pull/368">#368</a></li> <li>@EmmaCAndersson made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1731809217" data-permission-text="Title is private" data-url="https://github.com/nf-core/raredisease/issues/357" data-hovercard-type="pull_request" data-hovercard-url="/nf-core/raredisease/pull/357/hovercard" href="https://github.com/nf-core/raredisease/pull/357">#357</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/nf-core/raredisease/compare/1.0.0...1.1.0"><tt>1.0.0...1.1.0</tt></a></p> ramprasadn tag:github.com,2008:Repository/378880039/1.0.0 2023-06-01T15:59:15Z Aladdin <p>Merge pull request <a class="issue-link js-issue-link" href="https://github.com/nf-core/raredisease/pull/322">#322</a> from nf-core/dev</p> <p>Release 1.0.0</p> ramprasadn