3,913 research outputs found
nf-core/quantms: nf-core/quantms v1.1.0 - Berlin
No full textThese release includes the following major changes:
Bugfixes and speed increases in the OpenMS tools due to version update to 2.9.1
Improvements in logging by adding many more process.ids
Large restructuring of DIA branch to increase parallelizability
Better error handling in MSstats step plus new parameter to filter for MSstats' adjusted p-value in the plots
More efficient parsing of mzML statistics in a separate step
A clearer distinction between per-run and experiment-wide FDRs with one parameter for each
More test profiles including larger "full" tests
What's Changed
[Feature] New release cycle for 1.1 by @jpfeuffer in https://github.com/nf-core/quantms/pull/35
[Testing] Add test profile as alias to test_lfq by @jpfeuffer in https://github.com/nf-core/quantms/pull/36
Important! Template update for nf-core/tools v2.4 by @nf-core-bot in https://github.com/nf-core/quantms/pull/44
Add mimetype to input parameter in schema by @drpatelh in https://github.com/nf-core/quantms/pull/45
Major changes in the quantms package by @ypriverol in https://github.com/nf-core/quantms/pull/47
[Fix] links due to server change by @jpfeuffer in https://github.com/nf-core/quantms/pull/54
Dev by @fabianegli in https://github.com/nf-core/quantms/pull/55
reproduce conda channel setup failure by @fabianegli in https://github.com/nf-core/quantms/pull/56
Important! Template update for nf-core/tools v2.5.1 by @nf-core-bot in https://github.com/nf-core/quantms/pull/53
Tetsrun by @fabianegli in https://github.com/nf-core/quantms/pull/59
Important! Template update for nf-core/tools v2.6 by @nf-core-bot in https://github.com/nf-core/quantms/pull/60
Sync dev by @jpfeuffer in https://github.com/nf-core/quantms/pull/69
Merging-template by @jpfeuffer in https://github.com/nf-core/quantms/pull/70
Important! Template update for nf-core/tools v2.7.2 by @nf-core-bot in https://github.com/nf-core/quantms/pull/66
Major PR with integration changes. by @ypriverol in https://github.com/nf-core/quantms/pull/72
small fixing for review PR #48 by @ypriverol in https://github.com/nf-core/quantms/pull/74
Contribution to v1 1 by @fabianegli in https://github.com/nf-core/quantms/pull/76
More changes for review 1.1 release by @ypriverol in https://github.com/nf-core/quantms/pull/77
small format changes by @ypriverol in https://github.com/nf-core/quantms/pull/78
changes for link module preprocess_expdesign.nf by @ypriverol in https://github.com/nf-core/quantms/pull/79
Prepare for release by @fabianegli in https://github.com/nf-core/quantms/pull/80
Dev by @ypriverol in https://github.com/nf-core/quantms/pull/81
consensusID remove process_medium by @ypriverol in https://github.com/nf-core/quantms/pull/82
[Release] 1.1 by @ypriverol in https://github.com/nf-core/quantms/pull/48
New Contributors
@nf-core-bot made their first contribution in https://github.com/nf-core/quantms/pull/44
@drpatelh made their first contribution in https://github.com/nf-core/quantms/pull/45
@fabianegli made their first contribution in https://github.com/nf-core/quantms/pull/55
Full Changelog: https://github.com/nf-core/quantms/compare/1.0...1.1.
nf-core/pixelator: nf-core/pixelator v1.1.0
No full text<h2>What's Changed</h2>
<ul>
<li>Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/83</li>
<li>Update to pixelator 0.16.2 by @johandahlberg in https://github.com/nf-core/pixelator/pull/84</li>
<li>Remove a workaround for container issues, silence some warnings, update default resources by @fbdtemme in https://github.com/nf-core/pixelator/pull/85</li>
<li>Release pixelator 1.1.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/86, https://github.com/nf-core/pixelator/pull/87</li>
</ul>
<h3>Software dependencies</h3>
<p>| Dependency | Old version | New version |
| ----------- | ----------- | ----------- |
| <code>pixelator</code> | 0.15.2 | 0.16.2 |</p>
<blockquote>
<p><strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present.</p>
<p><strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present.</p>
<p><strong>NB:</strong> Dependency has been <strong>removed</strong> if new version information isn't present.</p>
</blockquote>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/pixelator/compare/1.0.3...1.1.0</p>
nf-core/riboseq: nf-core/riboseq v1.0.0 - Altruistic Aventurine
No full text<h2>What's Changed</h2>
<ul>
<li>Restart dev from a new template by @maxulysse in https://github.com/nf-core/riboseq/pull/2</li>
<li>Restart dev by @maxulysse in https://github.com/nf-core/riboseq/pull/3</li>
<li>Initialise testing and base template functionality by @pinin4fjords in https://github.com/nf-core/riboseq/pull/4</li>
<li>Fix lint by @maxulysse in https://github.com/nf-core/riboseq/pull/5</li>
<li>Important! Template update for nf-core/tools v2.11.1 by @nf-core-bot in https://github.com/nf-core/riboseq/pull/7</li>
<li>Preprocessing from rnaseq by @pinin4fjords in https://github.com/nf-core/riboseq/pull/8</li>
<li>Take rnaseq preprocessing workflow from nf-core by @pinin4fjords in https://github.com/nf-core/riboseq/pull/10</li>
<li>Important! Template update for nf-core/tools v2.12 by @nf-core-bot in https://github.com/nf-core/riboseq/pull/9</li>
<li>Add alignment via STAR + postprocessing by @pinin4fjords in https://github.com/nf-core/riboseq/pull/12</li>
<li>Nf core template merge 2.13 (manual) by @pinin4fjords in https://github.com/nf-core/riboseq/pull/32</li>
<li>Fix order of preprocessing steps by @pinin4fjords in https://github.com/nf-core/riboseq/pull/34</li>
<li>Sortmerna: index once by @pinin4fjords in https://github.com/nf-core/riboseq/pull/35</li>
<li>Bump bbsplit module to prevent index overwrites by @pinin4fjords in https://github.com/nf-core/riboseq/pull/36</li>
<li>Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/riboseq/pull/38</li>
<li>Integrate Ribo-TISH by @pinin4fjords in https://github.com/nf-core/riboseq/pull/39</li>
<li>Ribotricer orf prediction by @pinin4fjords in https://github.com/nf-core/riboseq/pull/40</li>
<li>Amend credits statement by @FelixKrueger in https://github.com/nf-core/riboseq/pull/41</li>
<li>Add alignment based quantification with Salmon by @pinin4fjords in https://github.com/nf-core/riboseq/pull/42</li>
<li>Add translational efficiency analysis with anota2seq by @pinin4fjords in https://github.com/nf-core/riboseq/pull/43</li>
<li>Fix lack of fastqc in multiqc report by @pinin4fjords in https://github.com/nf-core/riboseq/pull/44</li>
<li>Update CI from rnaseq, strip unused rnaseq components by @pinin4fjords in https://github.com/nf-core/riboseq/pull/45</li>
<li>Prerelease changes v1.0.0 by @pinin4fjords in https://github.com/nf-core/riboseq/pull/46</li>
<li>Remove stub option from download in CI by @pinin4fjords in https://github.com/nf-core/riboseq/pull/48</li>
<li>Fix CI by @pinin4fjords in https://github.com/nf-core/riboseq/pull/49</li>
<li>changed logos to the custom w/ ribosome by @JackCurragh in https://github.com/nf-core/riboseq/pull/51</li>
<li>updated changelog by @JackCurragh in https://github.com/nf-core/riboseq/pull/52</li>
<li>V1.0.0 release review fixes by @pinin4fjords in https://github.com/nf-core/riboseq/pull/50</li>
<li>Dev -> master for v1.0.0 by @pinin4fjords in https://github.com/nf-core/riboseq/pull/47</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@maxulysse made their first contribution in https://github.com/nf-core/riboseq/pull/2</li>
<li>@pinin4fjords made their first contribution in https://github.com/nf-core/riboseq/pull/4</li>
<li>@nf-core-bot made their first contribution in https://github.com/nf-core/riboseq/pull/7</li>
<li>@FelixKrueger made their first contribution in https://github.com/nf-core/riboseq/pull/41</li>
<li>@JackCurragh made their first contribution in https://github.com/nf-core/riboseq/pull/51</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/riboseq/commits/1.0.0</p>
nf-core/pixelator: nf-core/pixelator v1.2.0
No full text<h2>What's Changed</h2>
<ul>
<li>Template update for nf-core/tools v2.14.1 by @fbdtemme in https://github.com/nf-core/pixelator/pull/89</li>
<li>Update pixelator to 0.17.1 by @johandahlberg in https://github.com/nf-core/pixelator/pull/90</li>
<li>Set <code>process_high</code> to use 64GB of RAM and <code>process_high_memory</code> to use 128GB of RAM by @johandahlberg in https://github.com/nf-core/pixelator/pull/91</li>
<li>Minor documentation fixes by @johandahlberg in https://github.com/nf-core/pixelator/pull/92</li>
<li>Improve read renaming by @fbdtemme in https://github.com/nf-core/pixelator/pull/93</li>
<li>Release nf-core/pixelator 1.2.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/94</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/pixelator/compare/1.1.0...1.2.0</p>
nf-core/isoseq: nf-core/isoseq v1.1.5 - Byzantium Buzzard [02/08/2023]
No full textUpdate the pipeline to nf-core 2.9.
Add gnu/sort to sort annotation before uLTRA index
Update citations
Add background to pipeline png
Update modules
| Tool | Previous version | New version |
| -------------------- | ---------------- | ----------- |
| isoseq3 | 3.8.1 | 3.8.2 |
| lima | 2.6.0 | 2.7.1 |
| bamtools/convert | 2.5.1 | 2.5.2 |
| gstama/merge | 1.0.2 | 1.0.3 |
| uLTRA/index | 0.0.4.2 | 0.1 |
| uLTRA/align | 0.0.4.2 | 0.1 |
| samtools | 1.17 | 1.17 |
| gnu/sort | ---- | 8.25
nf-core/pixelator: nf-core/pixelator v1.0.2
No full text<h2>[<a href="https://github.com/nf-core/pixelator/releases/tag/1.0.2">1.0.2</a>] - 2023-11-20</h2>
<h3>Enhancements & fixes</h3>
<ul>
<li>[<a href="https://github.com/nf-core/pixelator/pull/70">PR #70</a>] - Fix loading of absolute paths and urls in input samplesheet</li>
</ul>
nf-core/metaboigniter: nf-core/metaboigniter v1.0.0 - Teal Rose
No full textThe initial release of nf-core/metaboigniter pipeline.
This release includes:
IPO parameter tuning
mass trace detection using XCMS or OpenMS
Retention time alignment and grouping
Adduct and isotope detection
Noise filtering using QC stability, blank filtering, and dilution series
Metabolite identification using FINGER:ID, MetFrag, CFM-ID, and Internal library
Normalization and transformatio
nf-core/rnasplice: nf-core/rnasplice 1.0.3
No full text<h2>What's Changed</h2>
<ul>
<li>Move read.table out of loop by @jma1991 in https://github.com/nf-core/rnasplice/pull/121</li>
<li>Stop R converting sample names with '-' in string by @jma1991 in https://github.com/nf-core/rnasplice/pull/124</li>
<li>Patch fix v1.0.3 by @jma1991 in https://github.com/nf-core/rnasplice/pull/125</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/rnasplice/compare/1.0.2...1.0.3</p>
nf-core/nascent: Usul
No full text<h3>Added</h3>
<ul>
<li><a href="https://github.com/nf-core/nascent/commit/1494fff2ecd8b498e19d7d0fa3f7ee0f71088ab4">1494fff</a> - Update pipeline template to <a href="https://github.com/nf-core/tools/releases/tag/2.12">nf-core/tools 2.12</a></li>
<li><a href="https://github.com/nf-core/nascent/commit/ec24cfb2646904bcc78379a071b50b53a855b9a9">ec24cfb</a> - Update pipeline template to <a href="https://github.com/nf-core/tools/releases/tag/2.11.1">nf-core/tools 2.11.1</a></li>
<li><a href="https://github.com/nf-core/nascent/commit/15b8ff31cd43ec2e330ce7958bd6d7d65529b4d3">15b8ff3</a> - Update pipeline template to <a href="https://github.com/nf-core/tools/releases/tag/2.11">nf-core/tools 2.11</a></li>
<li><a href="https://github.com/nf-core/nascent/commit/97121638eb77e175b912ff45a669426e532c5d7f">9712163</a> - Update pipeline template to <a href="https://github.com/nf-core/tools/releases/tag/2.10">nf-core/tools 2.10</a></li>
<li>[<a href="https://github.com/nf-core/nascent/pull/130">#130</a>] - AWS Mega Tests</li>
<li>[<a href="https://github.com/nf-core/nascent/pull/132">#132</a>] - Add Bowtie 2 as an aligner option</li>
</ul>
<h3>Changed</h3>
<ul>
<li>[<a href="https://github.com/nf-core/nascent/pull/117">#117</a>] - Use fromSamplesheet</li>
<li>Updating naming scheme to use things from the Dune universe</li>
</ul>
nf-core/metatdenovo: Metatdenovo first release 1.0.0
No full text<p>Release of nf-core/metatdenovo version 1.0.0</p>
- …
