Andreas Tille pushed to branch upstream at Debian Med / paleomix
Commits: 95b58c29 by Andreas Tille at 2019-09-11T09:21:12Z New upstream version 1.2.13.4 - - - - - 4 changed files: - CHANGES.md - docs/phylo_pipeline/usage.rst - paleomix/nodes/picard.py - paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml Changes: ===================================== CHANGES.md ===================================== @@ -1,5 +1,11 @@ # Changelog +## [1.2.13.4] - 2019-03-25 +### Fixed + - Improved detection of Picard versions in cases where 'java' + outputs additional text. + + ## [1.2.13.3] - 2018-11-01 ### Fixed - Fixed validation/read counting of pre-trimmed reads not including @@ -581,7 +587,8 @@ the (partially) updated documentation now hosted on ReadTheDocs. - Switching to more traditional version-number tracking. -[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...HEAD +[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...HEAD +[1.2.13.4]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...v1.2.13.4 [1.2.13.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3 [1.2.13.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2 [1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1 ===================================== docs/phylo_pipeline/usage.rst ===================================== @@ -22,15 +22,15 @@ To execute the pipeline, a command corresponding to the step to be invoked is us Samples ------- -The phylogenetic pipeline expects a number of samples to be specified. Each sample has a name, a gender, and a genotyping method:: +The phylogenetic pipeline expects a number of samples to be specified. Each sample has a name, a sex, and a genotyping method:: Samples: <GROUP>: SAMPLE_NAME: - Gender: ... + Sex: ... Genotyping Method: ... -Gender is required, and is used to filter SNPs at homozygous sex chromsomes (e.g. chrX and chrY for male humans). Any names may be used, and can simply be set to e.g. 'NA' in case this feature is not used. +Sex is required, and is used to filter SNPs at homozygous sex chromsomes (e.g. chrX and chrY for male humans). Any names may be used, and can simply be set to e.g. 'NA' in case this feature is not used. The genotyping method is either "SAMTools" for the default genotyping procedure using samtools mpileupe | bcftools view, or "Random Sampling" to sample one random nucleotide in the pileup at each position. This key may be left out to use the default (SAMTools) method. ===================================== paleomix/nodes/picard.py ===================================== @@ -239,7 +239,7 @@ def picard_command(config, command): requirement = versions.Requirement(call=params.finalized_call, name="Picard tools", - search=r"^(\d+)\.(\d+)", + search=r"\b(\d+)\.(\d+)\.\d+", checks=versions.GE(1, 137)) _PICARD_VERSION_CACHE[jar_path] = requirement ===================================== paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml ===================================== @@ -8,25 +8,25 @@ Project: # in 'ExcludeSamples' and 'FilterSingletons'. Samples: 06_3928A: - Gender: NA + Sex: NA DDR7602: - Gender: NA + Sex: NA LBUS5: - Gender: NA + Sex: NA M-0182896: - Gender: NA + Sex: NA NL07434: - Gender: NA + Sex: NA P13527: - Gender: NA + Sex: NA P13626: - Gender: NA + Sex: NA P17777: - Gender: NA + Sex: NA Pi1845A: - Gender: NA + Sex: NA Pi1889: - Gender: NA + Sex: NA # Specifies a set of regions of interest, each representing one or more # named regions in a reference sequence (e.g. genes) in BED format. View it on GitLab: https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6 -- View it on GitLab: https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6 You're receiving this email because of your account on salsa.debian.org.
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