[med-svn] [Git][med-team/q2-dada2][upstream] New upstream version 2021.8.0
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Sat Sep 18 19:07:18 BST 2021
Steffen Möller pushed to branch upstream at Debian Med / q2-dada2
Commits:
87950c40 by Steffen Moeller at 2021-09-18T20:00:04+02:00
New upstream version 2021.8.0
- - - - -
17 changed files:
- + .github/workflows/ci.yml
- − .travis.yml
- LICENSE
- README.md
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- q2_dada2/__init__.py
- q2_dada2/_denoise.py
- q2_dada2/_stats.py
- q2_dada2/_transformer.py
- q2_dada2/_version.py
- q2_dada2/assets/run_dada_paired.R
- q2_dada2/plugin_setup.py
- q2_dada2/tests/__init__.py
- q2_dada2/tests/test_denoise.py
- q2_dada2/tests/test_stats.py
- setup.py
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -0,0 +1,55 @@
+# This file is automatically generated by busywork.qiime2.org and
+# template-repos - any manual edits made to this file will be erased when
+# busywork performs maintenance updates.
+
+name: ci
+
+on:
+ pull_request:
+ push:
+ branches:
+ - master
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+ steps:
+ - name: checkout source
+ uses: actions/checkout at v2
+
+ - name: set up python 3.8
+ uses: actions/setup-python at v1
+ with:
+ python-version: 3.8
+
+ - name: install dependencies
+ run: python -m pip install --upgrade pip
+
+ - name: lint
+ run: |
+ pip install -q https://github.com/qiime2/q2lint/archive/master.zip
+ q2lint
+ pip install -q flake8
+ flake8
+
+ build-and-test:
+ needs: lint
+ strategy:
+ matrix:
+ os: [ubuntu-latest, macos-latest]
+ runs-on: ${{ matrix.os }}
+ steps:
+ - name: checkout source
+ uses: actions/checkout at v2
+ with:
+ fetch-depth: 0
+
+ - name: set up git repo for versioneer
+ run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+
+ - uses: qiime2/action-library-packaging at alpha1
+ with:
+ package-name: q2-dada2
+ build-target: dev
+ additional-tests: py.test --pyargs q2_dada2
+ library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.travis.yml deleted
=====================================
@@ -1,25 +0,0 @@
-dist: trusty
-sudo: false
-language: python
-before_install:
- - export MPLBACKEND='Agg'
- - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- - export MINICONDA_PREFIX="$HOME/miniconda"
- - bash miniconda.sh -b -p $MINICONDA_PREFIX
- - export PATH="$MINICONDA_PREFIX/bin:$PATH"
- - conda config --set always_yes yes
- - conda update -q conda
- - conda info -a
-install:
- - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
- - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
- - source activate test-env
- - conda install -q pytest-cov
- - pip install -q flake8 coveralls
- - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- - make install
-script:
- - make lint
- - make test-cov
-after_success:
- - coveralls
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2020, QIIME 2 development team.
+Copyright (c) 2016-2021, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
README.md
=====================================
@@ -1,6 +1,5 @@
-# DADA2 QIIME 2 plugin
+# q2-dada2
-[](https://travis-ci.org/qiime2/q2-dada2)
-[](https://coveralls.io/github/qiime2/q2-dada2?branch=master)
+
-This package contains the DADA2 QIIME 2 plugin. To learn how to use this, see https://qiime2.org.
+This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
\ No newline at end of file
=====================================
ci/recipe/conda_build_config.yaml deleted
=====================================
@@ -1,2 +0,0 @@
-python:
- - 3.6
=====================================
ci/recipe/meta.yaml
=====================================
@@ -1,6 +1,5 @@
{% set data = load_setup_py_data() %}
{% set version = data.get('version') or 'placehold' %}
-{% set release = '.'.join(version.split('.')[:2]) %}
package:
name: q2-dada2
@@ -21,6 +20,10 @@ requirements:
- python {{ python }}
- biom-format >=2.1.5,<2.2a0
- bioconductor-dada2 1.18.0
+ # the following pin is due to recent issues with versions of r-matrix
+ # past 1.3-2:
+ # https://github.com/benjjneb/dada2/issues/212#issuecomment-836757295
+ - r-matrix 1.3-2
# openjdk is not a real dependency, but, r-base has a post-link and post-
# activation hook that calls R CMD javareconf, which pokes around for any
# installations of java. On modern versions of macOS, a binary called
@@ -29,10 +32,15 @@ requirements:
# present. By including openjdk on osx hosts, this pop-up is prevented at
# installation and activation time of the environment.
- openjdk # [osx]
- - qiime2 {{ release }}.*
- - q2-types {{ release }}.*
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_dada2
- qiime2.plugins.dada2
=====================================
q2_dada2/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_denoise.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -65,6 +65,7 @@ _valid_inputs = {
'max_ee_f': _NAT_NUM,
'max_ee_r': _NAT_NUM,
'trunc_q': _WHOLE_NUM,
+ 'min_overlap': _WHOLE_NUM,
'max_len': _WHOLE_NUM,
'pooling_method': _POOL_STR,
'chimera_method': _CHIM_STR,
@@ -222,7 +223,8 @@ def denoise_paired(demultiplexed_seqs: SingleLanePerSamplePairedEndFastqDirFmt,
trunc_len_f: int, trunc_len_r: int,
trim_left_f: int = 0, trim_left_r: int = 0,
max_ee_f: float = 2.0, max_ee_r: float = 2.0,
- trunc_q: int = 2, pooling_method: str = 'independent',
+ trunc_q: int = 2, min_overlap: int = 12,
+ pooling_method: str = 'independent',
chimera_method: str = 'consensus',
min_fold_parent_over_abundance: float = 1.0,
n_threads: int = 1, n_reads_learn: int = 1000000,
@@ -257,7 +259,7 @@ def denoise_paired(demultiplexed_seqs: SingleLanePerSamplePairedEndFastqDirFmt,
str(trunc_len_f), str(trunc_len_r),
str(trim_left_f), str(trim_left_r),
str(max_ee_f), str(max_ee_r), str(trunc_q),
- str(pooling_method),
+ str(min_overlap), str(pooling_method),
str(chimera_method), str(min_fold_parent_over_abundance),
str(n_threads), str(n_reads_learn)]
try:
=====================================
q2_dada2/_stats.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (HEAD -> master, tag: 2020.11.1)"
- git_full = "7859a393b093170db097abb3dcc3aba05d72949a"
- git_date = "2020-12-05 20:44:45 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "6410e66cfebe29470f57c0bd9a5f072c5177c8b0"
+ git_date = "2021-09-09 18:35:33 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_dada2/assets/run_dada_paired.R
=====================================
@@ -129,11 +129,12 @@ trimLeftR <- as.integer(args[[10]])
maxEEF <- as.numeric(args[[11]])
maxEER <- as.numeric(args[[12]])
truncQ <- as.integer(args[[13]])
-poolMethod <- args[[14]]
-chimeraMethod <- args[[15]]
-minParentFold <- as.numeric(args[[16]])
-nthreads <- as.integer(args[[17]])
-nreads.learn <- as.integer(args[[18]])
+minOverlap <- as.integer(args[14])
+poolMethod <- args[[15]]
+chimeraMethod <- args[[16]]
+minParentFold <- as.numeric(args[[17]])
+nthreads <- as.integer(args[[18]])
+nreads.learn <- as.integer(args[[19]])
### VALIDATE ARGUMENTS ###
@@ -252,7 +253,7 @@ if(poolMethod == "pseudo") {
for(j in seq(length(filtsF))) {
drpF <- derepFastq(filtsF[[j]])
drpR <- derepFastq(filtsR[[j]])
- mergers[[j]] <- mergePairs(ddsF[[j]], drpF, ddsR[[j]], drpR)
+ mergers[[j]] <- mergePairs(ddsF[[j]], drpF, ddsR[[j]], drpR, minOverlap=minOverlap)
denoisedF[[j]] <- getN(ddsF[[j]])
cat(".")
}
=====================================
q2_dada2/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -136,6 +136,8 @@ plugin.methods.register_function(
'max_ee_f': qiime2.plugin.Float,
'max_ee_r': qiime2.plugin.Float,
'trunc_q': qiime2.plugin.Int,
+ 'min_overlap': qiime2.plugin.Int %
+ qiime2.plugin.Range(4, None),
'pooling_method': qiime2.plugin.Str %
qiime2.plugin.Choices(_POOL_OPT),
'chimera_method': qiime2.plugin.Str %
@@ -189,6 +191,8 @@ plugin.methods.register_function(
'read is then shorter than `trunc_len_f` or `trunc_len_r` '
'(depending on the direction of the read) it is '
'discarded.'),
+ 'min_overlap': ('The minimum length of the overlap required for '
+ 'merging the forward and reverse reads.'),
'pooling_method': ('The method used to pool samples for denoising. '
'"independent": Samples are denoised indpendently. '
'"pseudo": The pseudo-pooling method is used to '
=====================================
q2_dada2/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/tests/test_denoise.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_dada2/tests/test_stats.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-dada2/-/commit/87950c4018fcb8ddb6623de5a3ad88b3410205df
--
View it on GitLab: https://salsa.debian.org/med-team/q2-dada2/-/commit/87950c4018fcb8ddb6623de5a3ad88b3410205df
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