Commit 95b58c29 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.2.13.4

parent 48ed3c7f

CHANGES.md

+8 −1
Original line number Diff line number Diff line 
# 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

+3 −3
Original line number Diff line number Diff line
@@ -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

+1 −1
Original line number Diff line number Diff line
@@ -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

+10 −10
Original line number Diff line number Diff line
@@ -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.