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Recent Releases of rnaflow

rnaflow - 1.6.0

What's Changed

  • SortMeRNA refactor + update by @AggressiveHayBale in https://github.com/hoelzer-lab/rnaflow/pull/250

New Contributors

  • @AggressiveHayBale made their first contribution in https://github.com/hoelzer-lab/rnaflow/pull/250

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.5.1...1.6.0

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Published by hoelzer 8 months ago

rnaflow - 1.5.1

What's Changed

  • optimize CPU handling for hisat2 and more robust execution in HPC/Cloud settings by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/249

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.5.0...1.5.1

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Published by hoelzer 10 months ago

rnaflow - 1.5.0

What's Changed

  • fix strandness logic so that the CSV definition can be correctly overwritten by the --strand parameter by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/248

Fix strand value handling:

Previously, --strand 0 was interpreted as false in Groovy, preventing it from overwriting the CSV value. Now, the pipeline checks if --strand is set (non-empty), validates it (0, 1, or 2), and uses it if it differs from the CSV input. A warning is shown when values differ.

For example, this could have caused a problem when the CSV definition for Strandedness stated a value different from 0 and the pipeline was executed then with --strand 0. Then, the value in the CSV was not overwritten by --strand 0 (as intended); instead, the value in the CSV file was used.

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.9...1.5.0

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Published by hoelzer 10 months ago

rnaflow - 1.4.9

What's Changed

  • Fix tmp dir location for HISAT2 by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/247

ATTENTION: this made it necessary to update HISAT2 to the latest version and code base!

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.8...1.4.9

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Published by hoelzer 10 months ago

rnaflow - 1.4.8

What's Changed

  • add pbspro executor by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/233
  • automatically overwrite nf reports when resuming by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/244

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.7...1.4.8

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Published by hoelzer about 1 year ago

rnaflow - 1.4.7

What's Changed

  • Add Sus scrofa by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/231

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.6...1.4.7

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Published by hoelzer about 2 years ago

rnaflow - 1.4.6

What's Changed

  • Fix webgestalt missing organism by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/224

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.5...1.4.6

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Published by hoelzer over 2 years ago

rnaflow - Allowlist HTTP and HTTPS ENV in Singularity

On restricted HPCs (e.g. with SLURM) and when using Singularity, it can happen that Nextflow needs to pass specific environment configurations for allow-listed URLs to the Singularity containers. This can be achieved via

envWhitelist = "HTTPS_PROXY,HTTP_PROXY,http_proxy,https_proxy,FTP_PROXY,ftp_proxy"

In the nextflow.config which is now a default when using Singularity.

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Published by hoelzer over 2 years ago

rnaflow - Again, optimizing DESeq2 resources on HPC

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Published by hoelzer over 2 years ago

rnaflow - Optimize DESeq2 HPC resources

What's Changed

  • DESeq2 error handling, increase RAM on HPC by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/221

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.2...1.4.3

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Published by hoelzer over 2 years ago

rnaflow - SortMeRNA autoload hot fix

What's Changed

  • correct storage path of .tar.gz sortmerna files by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/220

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.1...1.4.2

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Published by hoelzer over 2 years ago

rnaflow - 1.4.1

What's Changed

  • update DGE result documentation by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/200
  • explicitly enable conda in conda profile by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/207
  • Fix deseq2 warnings ( use 'rowNames' instead of 'row.names' ) by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/208
  • Fix refactorreportingtoolstable.rb crash when run with non-ENS feature IDs and feature_type not 'gene' by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/210
  • Fix pca plots and ENS ID lookup for non-ENS IDs by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/209

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.4.0...1.4.1

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Published by hoelzer about 3 years ago

rnaflow - 1.4.0

Larger release adding various bug fixes, software updates, features, and customization options.

Special kudos @fischer-hub for all the help!

What's Changed

  • update multiqc to v1.12, add python v3.10 explicitly, closes #183 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/184
  • Parallelize deseq2.R script, closes #94 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/167
  • Fix report section order, closes #16 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/170
  • Setup mode support for conda and mamba by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/171
  • UpSet plots, deseq2 update, closes #10, closes #86 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/172
  • fix source col in README csv example, closes #173 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/180
  • fix bad character " ' " in gene names crashing deseq2.R , closes #177 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/189
  • fix channel order in expressionreferencebased sub-wf, closes #191 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/193
  • Strand parameter priority, closes #176 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/181
  • feature type is not considered and overwritten by feature attribute type by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/188
  • add node profile for cloud by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/174
  • fix typo by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/195
  • make webgestalt output optional by @hoelzer in https://github.com/hoelzer-lab/rnaflow/pull/196

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.3.0...1.4.0

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Published by hoelzer over 3 years ago

rnaflow - Version 1.3.0

What's Changed

  • add latency profile and documentation to pipeline, closes #79 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/155
  • Update tool versions and fix outdated DB links in processes dammit, busco by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/152
  • add full support for ONT-LR data in assembly sub-workflow, closes #150 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/157
  • Read auto detection, closes #76 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/158
  • fix pipeline crashing for long reads longer than 30k nt because of SMR, closes #162 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/164
  • new parameter --rna, closes #163 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/165
  • Generalize feature url retrieval in refactorreportingtoolstable.rb, closes #13 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/166
  • new parameter --setup to preload all DBs and ref files, closes #102 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/161
  • Skip read preprocessing (fastp), closes #100 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/160
  • add busco to multiqc, closes #85 by @fischer-hub in https://github.com/hoelzer-lab/rnaflow/pull/159
  • added mamba profile by @MarieLataretu in https://github.com/hoelzer-lab/rnaflow/pull/168
  • Fc flip report by @MarieLataretu in https://github.com/hoelzer-lab/rnaflow/pull/175

Full Changelog: https://github.com/hoelzer-lab/rnaflow/compare/1.2.5...1.3.0

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Published by MarieLataretu almost 4 years ago

rnaflow - Version 1.2.5

  • the comparison naming matches the logFC/counting numbers

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Published by MarieLataretu over 4 years ago

rnaflow - Version 1.2.4

Added build-in support for Rattus norvegicus

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Published by hoelzer over 4 years ago

rnaflow - Version 1.2.3

  • download SMR db only if necessary
  • small piano tweaks
  • fix #136

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Published by MarieLataretu over 4 years ago

rnaflow - Version 1.2.2

  • #126 fixed

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Published by MarieLataretu about 5 years ago

rnaflow - Version 1.2.1

  • fixes/sanity checks for input with no DEGs

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Published by MarieLataretu about 5 years ago

rnaflow - Version 1.2.0

  • some fixes for trinity (#121, #122)
  • fix for google cloud (#115)
  • removed params.workdir (#112)
  • more functionality for non-Ensembl annotations, introduced --feature_id_type (#110)

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Published by MarieLataretu about 5 years ago

rnaflow - Version 1.1.1

  • bug fix for piano cpus (see #109)
  • new parameter for featureCounts (see #118)
  • '--species' and --include_species are now deprecated and will be removed the next major release

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Published by MarieLataretu about 5 years ago

rnaflow - Version 1.1.0

some tweaks for the transcriptomics part

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Published by MarieLataretu about 5 years ago

rnaflow - Version 1.0.0

First release of RNAflow :tada:

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Published by MarieLataretu over 5 years ago