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bytesize_ nf-core Subworkflows.mp4
No full textMaxime Garcia shows us how to use the brand-new nf-core subworkflows!</p
Souvenirs et paysages d'Orient. Smyrne -Éphèse-Magnésie- Constantinople-Scio. Par Maxime du Paris chez. Arthus Bertrand, Libraire Editeur de la Société géographique 1848.
No full textPreface: by the authorDedication: by the author to B.F., S. ad. 5Content description: Detailed contentsPagination: PP10+380PVolumes: 1Text Genre:Prose / Journa
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/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/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/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/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/riboseq: nf-core/riboseq v1.0.1 - Augmented Aventurine
No full text<h2>What's Changed</h2>
<ul>
<li>Bump to v1.0.1 and set Zenodo by @pinin4fjords in https://github.com/nf-core/riboseq/pull/53</li>
<li>Add legal logos and first metro map by @FelixKrueger in https://github.com/nf-core/riboseq/pull/54</li>
<li>Prerelease v1.0.1 by @pinin4fjords in https://github.com/nf-core/riboseq/pull/55</li>
<li>fixed svgs to match the exported pngs by @JackCurragh in https://github.com/nf-core/riboseq/pull/57</li>
<li>Dev -> master for v1.0.1 by @pinin4fjords in https://github.com/nf-core/riboseq/pull/56</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/riboseq/compare/1.0.0...1.0.1</p>
nf-core/pixelator: nf-core/pixelator v1.0.1
No full text<h2>[<a href="https://github.com/nf-core/pixelator/releases/tag/1.0.1">1.0.1</a>] - 2023-10-27</h2>
<h3>Enhancements & fixes</h3>
<ul>
<li>[<a href="https://github.com/nf-core/pixelator/pull/66">PR #66</a>] - Add a warning and workaround for singularity & apptainer</li>
<li>Cleanup some linting warnings</li>
<li>Update docker image in RENAME_READS to match the singularity container</li>
</ul>
<h3>Software dependencies</h3>
<p>| Dependency | Old version | New version |
| ----------- | ----------- | ----------- |
| <code>pixelator</code> | 0.15.0 | 0.15.2 |</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>
nf-core/atacseq: nf-core/atacseq v2.1.0 - Iron Cow
No full text[2.1.0] - 2022-07-21
Credits
Special thanks to the following for their contributions to the release:
Adam Talbot
Björn Langer
Harshil Patel
Maxime Garcia
Rob Syme
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
Enhancements & fixes
[#226] - Add ataqv_mito_reference parameter.
Optional support of control data analog to nf-core/chipseq.
[#277] - Fix error when using a gunziped fasta file.
[#286] - Fix error when no `--mito_name parameter is provided.
[#268] - Fix error when a bed file is provided using the --blacklist option.
[#278] - Make genome fasta file available when IGV process is run.
[#276] - Bump version 1.3.1 of ataqv to fix enrichment plots rendering.
[#290] - Fix case-sensitivity issue while sorting bedGraph.
[#295] - Enable downstream steps for bam files produced from paired-end reads by chromap after its upgrade.
Updated pipeline template to nf-core/tools 2.9
Make fasta index available for IGV session.
[nf-core/chipseq#347] - Add read group tag to bam files processed by bowtie2
Parameters
Old parameter
New parameter
--with_control
--ataqv_mito_reference
NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if parameter information isn't present.
Software dependencies
Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
Dependency
Old version
New version
ataqv
1.3.0
1.3.1
chromap
0.2.1
0.2.4
multiqc
1.13
1.14
picard
2.27.4
3.0.0
samtools
1.15.1
1.17
ucsc-bedgraphtobigwig
377
445
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present
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