cellranger_mkfastq tagshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags2020-11-03T12:17:27-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.3.0rc2test_2.3.0rc2Fix typo in astrocyte.yamlVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.3.0rc1test_2.3.0rc1Testing new astrocyte version with singularityVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/publish_2.2.0publish_2.2.0<h3 data-sourcepos="1:1-1:10" dir="auto">
<a id="user-content-v220" class="anchor" href="#v220" aria-hidden="true"></a>v2.2.0</h3>
<p data-sourcepos="2:1-2:14" dir="auto"><strong>UserFacing</strong></p>
<ul data-sourcepos="3:1-4:0" dir="auto">
<li data-sourcepos="3:1-4:0">Update cellranger to version 4.0.0</li>
</ul>
<p data-sourcepos="5:1-5:14" dir="auto"><strong>Background</strong></p>
<ul data-sourcepos="6:1-8:0" dir="auto">
<li data-sourcepos="6:1-6:18">Add runtime info</li>
<li data-sourcepos="7:1-8:0">Make standard (profile) be biohpc AND cluster</li>
</ul>
<p data-sourcepos="9:1-9:12" dir="auto"><em>Known Bugs</em></p>
<ul data-sourcepos="10:1-15:131" dir="auto">
<li data-sourcepos="10:1-12:69">cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue <a href="https://github.com/10XGenomics/cellranger/issues/31" rel="nofollow noreferrer noopener" target="_blank">#31</a>
<ul data-sourcepos="11:5-12:69">
<li data-sourcepos="11:5-11:60">note: 10x doesn't check github issues, emailed instead</li>
<li data-sourcepos="12:5-12:69">note: pipeline checks for spaces and exits prematurely if found</li>
</ul>
</li>
<li data-sourcepos="13:1-14:95">If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
<ul data-sourcepos="14:5-14:95">
<li data-sourcepos="14:5-14:95">note: if multiple bcl files are detected then cellranger_count design file is not created</li>
</ul>
</li>
<li data-sourcepos="15:1-15:131">If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging</li>
</ul>2020-11-03T12:17:27-06:00Gervaise H. Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.2.0rc5test_2.2.0rc5Venkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.2.0rc4test_2.2.0rc4Venkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.2.0rc3test_2.2.0rc3Venkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.2.0rc2test_2.2.0rc2Venkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/test_2.2.0test_2.2.0Venkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/publish_2.1.5publish_2.1.5<h3 data-sourcepos="1:1-1:10" dir="auto">
<a id="user-content-v215" class="anchor" href="#v215" aria-hidden="true"></a>v2.1.5</h3>
<p data-sourcepos="2:1-2:14" dir="auto"><strong>UserFacing</strong></p>
<ul data-sourcepos="3:1-11:0" dir="auto">
<li data-sourcepos="3:1-3:56">Check Design File for spaces in name and file contents</li>
<li data-sourcepos="4:1-4:75">Update design example, README, and astrocyte.yml with current barcode IDs</li>
<li data-sourcepos="5:1-5:47">Remove unnecessary intermediate process files</li>
<li data-sourcepos="6:1-6:38">Add config option for running on AWS</li>
<li data-sourcepos="7:1-7:19">Ignore dual index</li>
<li data-sourcepos="8:1-8:58">Add parameter for base mask (not available in Astrocyte)</li>
<li data-sourcepos="9:1-9:38">Output Nextflow version in QC report</li>
<li data-sourcepos="10:1-11:0">Output pipeline version (manual) in QC report</li>
</ul>
<p data-sourcepos="12:1-12:14" dir="auto"><strong>Background</strong></p>
<ul data-sourcepos="13:1-16:0" dir="auto">
<li data-sourcepos="13:1-13:56">Add Nextflow Tower integration into CI (GHH's profile)</li>
<li data-sourcepos="14:1-14:32">Update to be runnable on cloud</li>
<li data-sourcepos="15:1-16:0">Refactor configs</li>
</ul>
<p data-sourcepos="17:1-17:12" dir="auto"><em>Known Bugs</em></p>
<ul data-sourcepos="18:1-23:131" dir="auto">
<li data-sourcepos="18:1-20:69">cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue <a href="https://github.com/10XGenomics/cellranger/issues/31" rel="nofollow noreferrer noopener" target="_blank">#31</a>
<ul data-sourcepos="19:5-20:69">
<li data-sourcepos="19:5-19:60">note: 10x doesn't check github issues, emailed instead</li>
<li data-sourcepos="20:5-20:69">note: pipeline checks for spaces and exits prematurely if found</li>
</ul>
</li>
<li data-sourcepos="21:1-22:95">If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
<ul data-sourcepos="22:5-22:95">
<li data-sourcepos="22:5-22:95">note: if multiple bcl files are detected then cellranger_count design file is not created</li>
</ul>
</li>
<li data-sourcepos="23:1-23:131">If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging</li>
</ul>2020-06-21T20:17:59-05:00Gervaise H. Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/containerizedcontainerizedThis is a fully containerized version of the pipelineGervaise H. Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/publish_1.3.1publish_1.3.1<h3 data-sourcepos="1:1-1:10" dir="auto">
<a id="user-content-v131" class="anchor" href="#v131" aria-hidden="true"></a>v1.3.1</h3>
<p data-sourcepos="2:1-2:15" dir="auto"><strong>User Facing</strong></p>
<ul data-sourcepos="3:1-8:0" dir="auto">
<li data-sourcepos="3:1-3:36">Change Cellranger Version to 3.1.0</li>
<li data-sourcepos="4:1-4:42">Fix countDesign to take multiple samples</li>
<li data-sourcepos="5:1-5:17">Add MIT License</li>
<li data-sourcepos="6:1-6:56">Check Design File for spaces in name and file contents</li>
<li data-sourcepos="7:1-8:0">Update design example, README, and astrocyte.yml with current barcode IDs</li>
</ul>
<p data-sourcepos="9:1-9:14" dir="auto"><strong>Background</strong></p>
<ul data-sourcepos="10:1-12:0" dir="auto">
<li data-sourcepos="10:1-10:18">Add CI artifacts</li>
<li data-sourcepos="11:1-12:0">Add Nextflow Tower integration into CI (GHH's profile)</li>
</ul>
<p data-sourcepos="13:1-13:12" dir="auto"><em>Known Bugs</em></p>
<ul data-sourcepos="14:1-18:95" dir="auto">
<li data-sourcepos="14:1-16:69">cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue <a href="https://github.com/10XGenomics/cellranger/issues/31" rel="nofollow noreferrer noopener" target="_blank">#31</a>
<ul data-sourcepos="15:5-16:69">
<li data-sourcepos="15:5-15:60">note: 10x doesn't check github issues, emailed instead</li>
<li data-sourcepos="16:5-16:69">note: pipeline checks for spaces and exits prematurely if found</li>
</ul>
</li>
<li data-sourcepos="17:1-18:95">If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
<ul data-sourcepos="18:5-18:95">
<li data-sourcepos="18:5-18:95">note: if multiple bcl files are detected then cellranger_count design file is not created</li>
</ul>
</li>
</ul>2020-06-20T20:55:57-05:00Gervaise H. Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/publish_1.2.0publish_1.2.0<h3 data-sourcepos="1:1-1:10" dir="auto">
<a id="user-content-v120" class="anchor" href="#v120" aria-hidden="true"></a>v1.2.0</h3>
<p data-sourcepos="2:1-2:15" dir="auto"><strong>User Facing</strong></p>
<ul data-sourcepos="3:1-6:0" dir="auto">
<li data-sourcepos="3:1-3:45">Add references to of tools to mutiQC report</li>
<li data-sourcepos="4:1-4:36">Add BICF details to multiqc report</li>
<li data-sourcepos="5:1-6:0">Create cellranger_count design file (if only 1 flowcell is inputted)</li>
</ul>
<p data-sourcepos="7:1-7:14" dir="auto"><strong>Background</strong></p>
<ul data-sourcepos="8:1-16:0" dir="auto">
<li data-sourcepos="8:1-8:26">Add DOI (develop branch)</li>
<li data-sourcepos="9:1-9:57">Add changelog as link to astrocyte docs (master branch)</li>
<li data-sourcepos="10:1-10:67">Update example design file link in astrocyte docs (master branch)</li>
<li data-sourcepos="11:1-11:129">Check tarballed bcl directory for spaces and exit if it contains one...cellranger mkfastq cannot handle spaces (develop branch)</li>
<li data-sourcepos="12:1-12:51">Move untar (including space check) to bash script</li>
<li data-sourcepos="13:1-13:35">Add Jeremy Mathews to author list</li>
<li data-sourcepos="14:1-14:19">Apply style guide</li>
<li data-sourcepos="15:1-16:0">Add pytests for ouptuts</li>
</ul>
<p data-sourcepos="17:1-17:12" dir="auto"><em>Known Bugs</em></p>
<ul data-sourcepos="18:1-22:95" dir="auto">
<li data-sourcepos="18:1-20:69">cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue <a href="https://github.com/10XGenomics/cellranger/issues/31" rel="nofollow noreferrer noopener" target="_blank">#31</a>
<ul data-sourcepos="19:5-20:69">
<li data-sourcepos="19:5-19:60">note: 10x doesn't check github issues, emailed instead</li>
<li data-sourcepos="20:5-20:69">note: pipeline checks for spaces and exits prematurely if found</li>
</ul>
</li>
<li data-sourcepos="21:1-22:95">If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
<ul data-sourcepos="22:5-22:95">
<li data-sourcepos="22:5-22:95">note: if multiple bcl files are detected then cellranger_count design file is not created</li>
</ul>
</li>
</ul>2020-06-20T20:55:27-05:00Gervaise H. Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/publish_1.1.4publish_1.1.4<h3 data-sourcepos="1:1-1:10" dir="auto">
<a id="user-content-v114" class="anchor" href="#v114" aria-hidden="true"></a>v1.1.4</h3>
<p data-sourcepos="2:1-2:15" dir="auto"><strong>User Facing</strong></p>
<ul data-sourcepos="3:1-5:0" dir="auto">
<li data-sourcepos="3:1-3:42">Fix design file not visible in Astrocyte</li>
<li data-sourcepos="4:1-5:0">Fix handling of multiple flowcells in 1 submission</li>
</ul>
<p data-sourcepos="6:1-6:14" dir="auto"><strong>Background</strong></p>
<ul data-sourcepos="7:1-11:0" dir="auto">
<li data-sourcepos="7:1-7:36">Move multiqc config to conf folder</li>
<li data-sourcepos="8:1-8:36">Add CI test for multiple flowcells</li>
<li data-sourcepos="9:1-9:15">Add changelog</li>
<li data-sourcepos="10:1-11:0">Quote design/tarball/$baseDir path in processes in case of spaces</li>
</ul>
<p data-sourcepos="12:1-12:12" dir="auto"><em>Known Bugs</em></p>
<ul data-sourcepos="13:1-13:192" dir="auto">
<li data-sourcepos="13:1-13:192">cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue <a href="https://github.com/10XGenomics/cellranger/issues/31" rel="nofollow noreferrer noopener" target="_blank">#31</a>
</li>
</ul>2020-06-20T20:54:59-05:00Gervaise H. Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/tags/publish_1.0.0publish_1.0.0<p data-sourcepos="1:1-1:34" dir="auto">Initial Astrocyte deployed version</p>2020-06-20T20:54:17-05:00Gervaise H. Henrygervaise.henry@utsouthwestern.edu