Release notes¶
v1.2.0 - 2021-12-¶
- Main release:
-
- Add plugin support
- Add plugin documentation
- Update Flye from 2.7 to 2.8
- Update Go from 1.13 to 1.17
- Add Winnowmap plugin (tested with v2.03-3-gf9a4c1a)
- Update Ubuntu in Singularity from 18.04 to 20.04
- Remove Deepbinner demultiplexing module
- Remove Albacore support (deprecated by ONT, outperformed by guppy)
- Remove Flappie basecaller support (rules remain, builds are disabled)
- All-in-one Docker build (docker.com/nanopype/nanopype) is temporarily disabled
- Add CONDA_PREFIX to cmake paths (#21)
v1.1.0 - 2020-09-16¶
- Maintenance release:
-
- Fix nanopolish install (eigen lib moved to gitlab)
- Update Nanopolish to v0.13.2
- Fix single read methylation bam for secondary alignments (minimap2)
- Fix pdf report alignment part (#20)
- Add standalone vbz compression installation
v1.0.1 - 2020-08-04¶
- Maintenance release:
-
- Fix data & reference mount in singularity container
- Fix python module installations in source mode (affects deepbinner, svim, flye and pychopper)
v1.0.0 - 2020-07-28¶
- Main release:
-
- Rewrite and automate unit tests for source, Singularity and Docker
- Move Docker builds to travis-ci
- The all-in-one Docker has moved to docker://nanopype/nanopype
- Update Guppy to v4.0.11
- Update GraphMap to GraphMap2 v0.6.4
- Update Pychopper to v2.4.0
- Add wtdbg2 v2.5 (closes #8)
- Add svim v1.4.0
- Improve and extend the tutorial
- Add contributions section
- Fix snakemake file exists error in case of raw data relative to workdir
- Fix Flappie basecalling "cat: methyl_marks.tsv: No such file or directory"
- Fix Flappie basecalling with fastq output
- Fix GraphMap and NGMLR index for .fasta extension (worked for .fa only)
- Fix methylation detection re-running in NGMLR workflow (fixes #9)
- Fix single read methylation .bam for references with whitespace in name
v0.11.1 - 2020-06-18¶
- Maintenance release:
-
- Fix all-in-one Docker build
v0.11.0 - 2020-06-17¶
Main release:
- The output of nanopype >= v0.11.0 is limited backwards compatible.
- The methylation module was reworked, while output files are identical, the format of
- temporary files changed.
- Please run
rm methylation/*/*/*/batches/*/*/*.tsv
in each working directory, - to remove previous files.
- Nanopype >= v0.11.0 requires a Python >=3.6 installation.
-
- PDF reports are back without pdflatex backend and with more plots!
- Add onerror and onsuccess handler to workflow
- Log each pipeline run with config and file system changes
- Replace ont_fast5_api submodule with pip package
- Always install go with the pipeline
- Rework methylation module to get batch files with consistent format
- Rework single read methylation script to benefit from multiple cores
- Fix Flye build in source installation
- Known issues:
-
- The Flappie basecaller is temporarily excluded from the singularity builds due to build errors. Flappie will still work if installed manually.
v0.10.0 - 2020-02-10¶
- Main release:
-
- Introduce assembly module with flye
- Enable guppy GPU mode via basecall_server
- Flye v2.6
- Update guppy_basecaller and guppy_barcoder to version v3.4.4
- The basecalling module is simplified to support only .fastq.gz extension. (instead of fastq, fq, fasta, fa)
- The analysis singularity container is deprecated due to its size (4G) and complex pdflatex dependencies. Better pdf reports and logs are the objective of v0.11.0.
v0.9.1 - 2019-11-13¶
- Maintenance release:
-
- Add rule for coverage track in bigWig format (alignment module)
- Merge basecall files (fastx) from list of filenames to avoid temporary files
- Merge alignment files (bam) from list of filenames, handle systems ulimit with partial merges
- Pin snakemake to version 5.5.2
- Upgrade go in transcript container to 1.13.4
v0.9.0 - 2019-08-30¶
- Main release:
-
- Add guppy_barcoder to workflows for sequence based demultiplexing
- Improve singularity handling by auto-mounting raw data and reference folders
- Document singularity user installation
- Fix bug in demultiplexing rules when using singularity (issue #5)
- Fix merge of bam batches for many files
- Fix wrong singularity paths in methylation module
v0.8.0 - 2019-07-01¶
- Main release:
-
- Allow customization of runtime and memory requirements for cluster computing (env.yaml)
- Update guppy_basecaller to version 3.1.5
- Change guppy config from flow-cell/kit to cfg file
- Fix guppy installation in Docker
- Improve Docker installation and tutorial documentation
v0.7.0 - 2019-05-16¶
- Development release:
-
- Update guppy_basecaller to version v3.0.3
- Move guppy installation into separate directory
- Fix demultiplexing rule raw data fetching
- Add doc section on updating the pipeline
- Minor documentation edits
v0.6.0 - 2019-04-30¶
Development release:
- The output of nanopype >= v0.6.0 is not backwards compatible due to major changes in the output filesystem structure.
-
- Introduce tag-concept to re-run the same workflow under different conditions
- Transparent demultiplexing with 'special' tags
- Rules to clean up batch data
- Enhance documentation on singularity usage
- Include STRique version v0.3.0
- Update Pychopper to version v0.5.0
- Update guppy_basecaller to version v2.3.7
v0.5.0 - 2019-03-26¶
Development release:
- The output of nanopype >= v0.5.0 is not backwards compatible due to major changes in the output filesystem structure.
-
- Rework alignment module to support sequence post-processing
- Enable Pinfish package for isoform detection
v0.4.1 - 2019-03-15¶
- Development release:
-
- Update guppy_basecaller to version v2.3.5
v0.4.0 - 2019-03-13¶
Development release:
- Version 0.4.0 is the singularity and bulk-fast5 release.
-
- Setup singularity images for each module
- Support both, .tar of single fast5 and bulk-fast5 of current MinKNOW versions
- Enhance documentation details on installation and cluster usage
v0.3.0 - 2019-02-05¶
Development release:
- The output of nanopype >= v0.3.0 is not backwards compatible due to major changes in the output filesystem structure.
-
- Fix guppy installation instructions to not overwrite existing library installations
- Apply general output structure of tool2/tool1/runs/runname.x to all processing chains (see module documentation/tutorial for details).
v0.2.1 - 2019-01-28¶
- Development release:
-
- Parse experimental Flappie methylation calls to bedGraph/bigWig
- Detect bigWig coverage from wildcards without requiring config entry
- Known issues:
-
- Installing guppy after flappie is overwriting a symlink to libhdf5.so causing the flappie basecaller to load a hdf5 library it was not linked to. This will be fixed in a future release by separating the libraries properly.
v0.2.0 - 2019-01-21¶
- Development release:
-
- Nanopolish v0.11.0
- htslib v1.9
- OpenBLAS v0.3.4
v0.1.0 - 2018-12-24¶
- Initial release with tool versions (for development or untagged repositories, the master branch with the tested version in brackets is used):
-
- Bedtools v2.27.1
- Samtools v1.9
- UCSCTools
- bedGraphToBigWig v4
- Flappie master (1.1.0-9ef4edf)
- Minimap2 v2.14-r883
- GraphMap master (v0.5.2)
- NGMLR v0.2.7
- Sniffles v1.0.10
- Deepbinner v0.2.0
Manual installations of albacore and guppy can't be versioned. The pipeline was tested with albacore 2.3.3 and guppy 2.1.3.