The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
New entrypoint option to skip isoseq pre-processing. Update the pipeline to nf-core 2.14.1. Update modules. nf-validation version pinned PR25 Upgrade from isoseq3 to isoseq (version 4) Fix segmentation fault PR27 Add alternative entrypoint PR10
A new entreypoint system has been implemented to allow the user where to start the analysis.
The isoseq entrypoint runs the full pipeline.
The map entrypoint runs the pipeline from the mapping step.
This new entreypoint option make possible to use the isoseq pipeline for analysis PacBio data when subreads are not provided, or for users who want to benefit from the mapping + TAMA analysis for their Nanopore data.
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Update modules to their nf-test version (bamtools/convert, custom/dumpsoftwareversions, gnu/sort, gstama/collapse/ gstama/merge, gstama/polyacleanup, gunzip, isoseq/refine, lima, minimap2/align, pbccs,ultra/align, ultra/index)
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Since isoseq3 switch to version 4, it has been rename isoseq
Tool Previous version New version bamtools/convert 2.5.2 2.5.2 isoseq 3.8.2 4.0.0 lima 2.7.1 2.9.0 minimap2/align 2.24 2.28 gnu/sort 8.25 9.3 multiqc 1.21 1.24.1
Update the pipeline to nf-core 2.9.
- Add gnu/sort to sort annotation before uLTRA index
- Update citations
- Add background to pipeline png
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
- Update minimap2 path test: Don't set gtf option. It is not expected to be used with minimap2 is chosen.
- FIX: Don't prepare gtf channel when minimap2 is chosen.
- Fix pipeline image path
- params.input invalid type if pipeline is run with local file in samplesheet (was working with URL)
- Fix issue #17. Thanks to Husen M. Umer.
- Zenodo DOI
- Update to template v2.7.2
- Remove hard coded capped option for GSTAMA_FILELIST step. Now follow user choice. Thanks to Mazdak Salavati.
| Tool | Previous version | New version |
|---|---|---|
| isoseq3 | 3.4.0 | 3.8.1 |
| lima | 2.2.0 | 2.6.0 |
| minimap2 | 2.21 | 2.24 |
| samtools | 1.12 | 1.14 |
| multiqc | 1.13 | 1.14 |
| pbccs | 6.2.0 | 6.4.0 |
| ultra_bioinformatics | 0.0.4 | 0.0.4.2 |
| samtools | 1.15.1 | 1.16.1 |
Update the pipeline to nf-core 2.5.1, update modules, and fix documentation.
- Documentation: Correct aligner option documentation
- Update
samplesheet_checkmodule - Update
dumpsoftwareversionmodule - Update
MultiQCmodule
Improves computation time.
Split uLTRA pipeline into two processes, uLTRA index and uLTRA align. GTF index is computed once and not chunk times.
uLTRA align sort and convert sam output into bam files. Aligned reads are already sorted by minimap2 module. Therefore, samtools sort module is not needed anymore and has been removed.
The bioperl module objective was to deal with spurious alignments produced by uLTRA if a malformed GTF is used. Removing it will stop the pipeline in case of malformed GTF.
Module resource requirements have been revised for four modules (gstama/merge, isoseq3/refine, lima, ultra/align) to reduce requested resources.
AWS runs with shows better run time and CPU/RAM usage (Results).
- Add
uLTRA indexanduLTRA alignto replaceuLTRA pipelinePR 1830 - Module resources adjustments:
gstama/merge,isoseq3/refine,lima,ultra/alignPR1858,gunzip,MultiQC
- Remove
uLTRA pipeline - Remove
samtools sortmodule - Remove
bioperlmodule
Initial release of nf-core/isoseq, created with the nf-core template.