1.4.7

What's Changed

• Add Sus scrofa by @hoelzer in #231

Full Changelog: 1.4.6...1.4.7

1.4.6

What's Changed

• Fix webgestalt missing organism by @fischer-hub in #224

Full Changelog: 1.4.5...1.4.6

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.

Again, optimizing DESeq2 resources on HPC

Update nodes.config

Further increase RAM for DESeq2 in error case

Optimize DESeq2 HPC resources

What's Changed

• DESeq2 error handling, increase RAM on HPC by @hoelzer in #221

Full Changelog: 1.4.2...1.4.3

SortMeRNA autoload hot fix

What's Changed

• correct storage path of .tar.gz sortmerna files by @hoelzer in #220

Full Changelog: 1.4.1...1.4.2

1.4.1

What's Changed

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

Full Changelog: 1.4.0...1.4.1

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

Full Changelog: 1.3.0...1.4.0

Version 1.3.0

What's Changed

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• Update tool versions and fix outdated DB links in processes dammit, busco by @fischer-hub in #152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

Full Changelog: 1.2.5...1.3.0

Version 1.2.5

• the comparison naming matches the logFC/counting numbers