v 2.0.0 - 2022-05-31 Aqua Zinc Chihuahua
v2.0.0 - 2022-05-31 Aqua Zinc Chihuahua
Major enhancements
- Updated pipeline template to nf-core/tools 2.4.1
- [#137] - Update mirtop container to version
0.4.25to fix multiqc error - Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
- Bump minimum Nextflow version from
20.04.0->21.10.3 - Point to the proper test data branch
- Software version(s) will now be reported for every module imported during a given pipeline execution
- Updated
nextflow_schema.jsonshould now display correctly on Nextflow Tower - Added mirtop logs to multiqc
- Allow a gene to be associated to a non null number of reads in all samples (in
edgeR_miRBase.rscript)
Other enhancements & fixes
- #134 - Fixed colSum of zero issues for edgeR_miRBase.R script
- #55 - update seqcluster to fix UMI-detecting bug
Parameters
| Old parameter | New parameter |
|---|---|
--conda |
--enable_conda |
--clusterOptions |
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 |
|---|---|---|
bioconductor-edger |
3.26.5 | 3.36.0 |
bioconductor-limma |
3.40.2 | 3.50.0 |
mirdeep2 |
2.0.1.2 | 2.0.1.3 |
mirtop |
0.4.23 | 0.4.25 |
multiqc |
1.10.1 | 1.12.0 |
python |
3.7.3 | 3.8.3 |
r-base |
3.6.3 | 4.0.3 |
r-data.table |
1.12.4 | 1.14.2 |
r-gplots |
3.0.1.1 | 3.1.1 |
r-statmod |
1.4.32 | 1.4.36 |
samtools |
1.12 | 1.13 |
seqcluster |
1.2.7 | 1.2.9 |
seqkit |
0.16.0 | 2.0.0 |
trim-galore |
0.6.6 | 0.6.7 |
bioconvert |
- | 0.4.3 |
htseq |
- | - |
markdown |
- | - |
pymdown-extensions |
- | - |
pygments |
- | - |
r-r.methodss3 |
- | - |
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.
What's Changed in terms of PRs
- bump version to 1.2.0dev by @KevinMenden in #92
- fix errors in miRDeep2 analysis when reads map to unplaced contigs in $refgenome by @Daniel-VM in #100
- Allow a gene to have reads in all samples in the edgeR analysis by @sdjebali in #93
- DSL2 update, mostly schema and config, a few linting items by @klkeys in #111
- DSL2: updated modules by @klkeys in #112
- migration to DSL2 by @lpantano in #104
- Important! Template update for nf-core/tools v2.1 by @nf-core-bot in #101
- Add new version syntax based on yml files to the pipeline by @JoseEspinosa in #119
- fix testdata file by @lpantano in #120
- Samplesheet versioning by @JoseEspinosa in #121
- Merge template 2.2 and update to latest DSL2 syntax by @JoseEspinosa in #125
- Important! Template update for nf-core/tools v2.2 by @nf-core-bot in #123
- Update modules, bump multiqc version and other minor fixes by @JoseEspinosa in #129
- Fix #134 by @apeltzer in #136
- Merging template updates 2.3 by @JoseEspinosa in #141
- Important! Template update for nf-core/tools v2.3.2 by @nf-core-bot in #138
- Update publishDir mode by @JoseEspinosa in #142
- Bump mirtop version 0.4.25 by @JoseEspinosa in #143
- Fix seqcluster umi bug by @abartlett004 in #144
- Merging template 2.4.0 by @JoseEspinosa in #148
- Important! Template update for nf-core/tools v2.4 by @nf-core-bot in #147
- Fix zenodo link and update changelog by @JoseEspinosa in #150
- Fix linting by @JoseEspinosa in #157
- Update mirdeep2_run.nf by @wbau in #154
- PR for 2.0.0 by @apeltzer in #151
New Contributors
- @Daniel-VM made their first contribution in #100
- @klkeys made their first contribution in #111
- @JoseEspinosa made their first contribution in #119
- @abartlett004 made their first contribution in #144
- @wbau made their first contribution in #154
Full Changelog: 1.1.0...2.0.0
