Nanopype v1.1.0

Main 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 vcf compression installation

Nanopype v1.0.0

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

Nanopype v0.11.1

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

Nanopype v0.10.0

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.

Nanopype v0.9.1

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

Nanopype v0.9.0

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

Nanopype v0.8.0

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

Nanopype v0.7.0

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

Nanopype v0.6.0

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

Nanopype v0.5.0

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