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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 ( 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 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.