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ChangeLog
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Changelog
=========
0.1-alpha.15 (2015-09-29)
-------------------------
- Add final support for bokehutils-0.1.6. [Per Unneberg]
Fix #46
- Minor changes to ATAC-seq. [Per Unneberg]
- make picard summary pick up unique files
- add ucsc to ATAC-seq workflow
- Use log2 values for pca plots. [Per Unneberg]
- Pickle pca output, minor changes to templates. [Per Unneberg]
- Add pca plots and templates. [Per Unneberg]
Substantial additions including:
- code to do pca and plot the results
- template additions
- minor fixes to the ordering on x-axes
- Minor fixes. [Per Unneberg]
- Add and update pca rule. [Per Unneberg]
- Add release notes for 0.1-alpha.15. [Per Unneberg]
- Convert numerical sample ids to strings. [Per Unneberg]
Fixes #45
- Update dependency to bokehutils-0.1.6. [Per Unneberg]
- update templates to use bokeh_css and bokeh_js
- Remove dirty tags from doc build. [Per Unneberg]
Fixes #47
0.1-alpha.14 (2015-09-16)
-------------------------
- Update dependency to snakemake 3.4.2. [Per Unneberg]
- Disable limit in find_files. [Per Unneberg]
Disable limit in find_files if limit key missing in regexp
0.1-alpha.13 (2015-09-10)
-------------------------
- Hotfix: fix #40. [Per Unneberg]
scrnaseq merge rule did symlink on temporary dependency
0.1-alpha.12 (2015-09-08)
-------------------------
- Make correct rnaseq annotations. [Per Unneberg]
Fix #39
0.1-alpha.11 (2015-09-07)
-------------------------
- Add release notes. [Per Unneberg]
- Update rules to work standalone. [Per Unneberg]
- Move data and include in setup. [Per Unneberg]
Add db lambda functions and update docs
Documentation update
Documentation update
- Documentation updates. [Per Unneberg]
- Minor tweaks to rules and workflow. [Per Unneberg]
- Update navbar and add sidebar toc. [Per Unneberg]
- Ditto. [Per Unneberg]
- Updates to docs. [Per Unneberg]
- Documentation updates. [Per Unneberg]
- Minor fixes to rules. [Per Unneberg]
- Convert bamtools to atomic and fix rules. [Per Unneberg]
Convert bamtools to atomic rules. Fix some bugs in rules.
- Fixes for scrnaseq workflow. [Per Unneberg]
- add reporting rules for rseqc, rsem, star
- update cloudbiolinux annotation gtf rule
- Cleanup python2 statements. [Per Unneberg]
Statements have been pruned of " && "
- Simplify bowtie2_align. [Per Unneberg]
Can take gzipped input
- Update config loading. [Per Unneberg]
- change sml_path and friends to variables (fixes #38)
- remove trailing refs to samtools_cfg and the likes (fixes #37)
0.1-alpha.10 (2015-09-01)
-------------------------
- Add snakemakelib.workflow to setup. [Per Unneberg]
Fixes #34
0.1-alpha.9 (2015-08-31)
------------------------
- Update aligner config in atacseq. [Per Unneberg]
Fixes #23
0.1-alpha.8 (2015-08-30)
------------------------
- Add release notes. [Per Unneberg]
cdb40d0 fixes #21
- Add readthedocs test based on file name. [Per Unneberg]
- Add error message. [Per Unneberg]
- Add socket to get hostname. [Per Unneberg]
- Remove matplotlib dependency. [Per Unneberg]
0.1-alpha.7 (2015-08-29)
------------------------
- Add release notes. [Per Unneberg]
- Remove trailing diff line. [Per Unneberg]
- Add atomic_rules. [Per Unneberg]
Fixes #12
Fix various inconsistensies in workflows
- Add angsd and tuxedo atomic rules. [Per Unneberg]
- Add misc atomic rules. [Per Unneberg]
- Add vcftools. [Per Unneberg]
- Add atomic variation rules. [Per Unneberg]
Add rules for annovar, snpeff, htslib, vcftools, vcf
- Add rsem atomic rules. [Per Unneberg]
- Add rpkmforgenes atomic rules. [Per Unneberg]
- Delete sequenceprocessing and convert to single applications. [Per
Unneberg]
- Add cutadapt atomic rules. [Per Unneberg]
- Add rseqc atomic rules. [Per Unneberg]
- Add picard atomic rules. [Per Unneberg]
- Add gatk atomic rules. [Per Unneberg]
- Add and update atomic rules. [Per Unneberg]
- Add atomic rules. [Per Unneberg]
Start converting to atomic rules
- Initial support of atomic rules. [Per Unneberg]
* setup.py: distinguish between multiple rules and atomic rules with '.rule' and '.rules' suffixes
* snakemakelib/config.py: don't require config dict is a BaseConfig instance
* snakemakelib/rules/bio/ngs/align/bwa/bwa.rules: default settings for bwa
* snakemakelib/rules/bio/ngs/align/bwa/bwa_index.rule: atomic bwa index rule
* snakemakelib/rules/bio/ngs/align/bwa/bwa_link_ref.rule: atomic bwa link ref rule
* snakemakelib/rules/bio/ngs/align/bwa/bwa_mem.rule: atomic bwa mem rule
* snakemakelib/rules/bio/ngs/settings.rules: use tentative snakemake configdefault keyword
* snakemakelib/rules/bio/ngs/tools/samtools.rules: ditto
* snakemakelib/rules/settings.rules: ditto
- Update bokehutils dependency. [Per Unneberg]
Fix #22
- Reuse matplotlib >= 1.4.0. [Per Unneberg]
- Test matplotlib 1.4.0. [Per Unneberg]
- Readd matplotlib dependency. [Per Unneberg]
- Revert conf and remove matplotlib dependency. [Per Unneberg]
- Mock: alternative take. [Per Unneberg]
- Mock matplotlib for documentation build. [Per Unneberg]
Attempt to fix #21
- Fix errors in readme. [Per Unneberg]
- Misc fixes. [Per Unneberg]
- remove test doc files
- readd load_sml_config
0.1-alpha.6 (2015-08-25)
------------------------
- Add release notes. [Per Unneberg]
- Delete travis test branch. [Per Unneberg]
- Remove superfluous test line. [Per Unneberg]
- Add pytest to setup. [Per Unneberg]
- Make py.test default test. [Per Unneberg]
- Use update_config. [Per Unneberg]
Minor fix.
Fixes #18 and #19
- Use update_config throughout. [Per Unneberg]
- for multiple update_config calls, need specific config_default dicts
for each call (otherwise config points to a reference)
- Make unique test file names. [Per Unneberg]
py.test best practices recommends unique file names
See http://stackoverflow.com/questions/12582503/py-test-test-discovery-failure-when-tests-in-different-directories-are-called
- Adapt tests to pytest. [Per Unneberg]
- add fixtures
- remove trailing refs to BaseConfig, update_snakemakelib_config
- Remove obsolete BaseConfig. [Per Unneberg]
Fixes #19
- Remove update_snakemake_config. [Per Unneberg]
- Remove update_snakemake_config and use update_config
- Also change update order to update_config(config_default, config)
- Follow pytest best practices and omit __init__.py. [Per Unneberg]
See https://pytest.org/latest/goodpractises.html#choosing-a-test-layout-import-rules
- Add support for pytest. [Per Unneberg]
Add pytest. Avoid running slow test. Note that tests are still based on
nose.
- Add update_config. [Per Unneberg]
- add update_config
- remove deprecated functions
0.1-alpha.5 (2015-07-22)
------------------------
- Fix erroneous tag prefix. [Per Unneberg]
* snakemakelib/_version.py: update tag_prefix
0.1.0-alpha.4 (2015-07-11)
--------------------------
- Add import of static_html. [Per Unneberg]
- Add plot dependencies. [Per Unneberg]
- Update docs, make editable install for coveralls. [Per Unneberg]
- Remove bokehutils and bokeh dependencies from setup.py. [Per Unneberg]
- Remove matplotlib. [Per Unneberg]
* setup.py: remove matplotlib to avoid pytz issue
* snakemakelib/rules/bio/ngs/enrichment/macs.rules: make BAMPE default input
- Undo editable install. [Per Unneberg]
* requirements.txt: remove -e flag
* setup.py: readd matplotlib
- Remove setup develop and readd nose.collector. [Per Unneberg]
- Change install order of bokeh and bokehutils. [Per Unneberg]
* requirements.txt: install bokehutils after .
* setup.py: add bokeh
- Update installation instructions. [Per Unneberg]
- Correct erroneous parameter call to fig.circle. [Per Unneberg]
* snakemakelib/bio/ngs/qc/cutadapt.py: move title to figure setup
* setup.py: depend on bokehutils 0.1.3
- * setup.py: add setup_requires. [Per Unneberg]
- * setup.py: add bokehutis to requires. [Per Unneberg]
- * requirements.txt: add -e flag to bokehutils. [Per Unneberg]
- * setup.py: remove erroneous test path. [Per Unneberg]
- * setup.py: remove bokehutils from requires. [Per Unneberg]
- Update versioneer and add tests. [Per Unneberg]
* setup.cfg: add versioneer
* setup.py: delete versioneer, add test modules
0.1.0-alpha.3 (2015-07-10)
--------------------------
- Update jinja template path. [Per Unneberg]
Fix #14
0.1.0-alpha.2 (2015-07-10)
--------------------------
- Update package data structure. [Per Unneberg]
* requirements.txt: use implementation recommended by https://caremad.io/blog/setup-vs-requirement/
* setup.py: model after bokeh setup - explicitly list packages and add requirements here
* snakemakelib/config.py: fix root path
0.1.0-alpha.1 (2015-07-09)
--------------------------
- Add samopt parameter for bowtie vs bowtie2. [Per Unneberg]
Fixes #11
- Add release notes doc. [Per Unneberg]
- Add bamtools filter on regions. [Per Unneberg]
- add regions options to bamtools filter
- add bamfilter to ATAC-seq workflow
- Bowtie2 index. [Per Unneberg]
Ditto in db
- Bowtie2 index. [Per Unneberg]
Make index function point to bowtie2 location
- Strip -e from install_requires. [Per Unneberg]
- Change git checkout to https. [Per Unneberg]
- Fix typo in requirements.txt. [Per Unneberg]
- Fix git installation syntax. [Per Unneberg]
- Setup bokehutils git requirement in requirements.txt. [Per Unneberg]
- * requirements.txt: require bokehutils==0.1.1 * .travis.yml: process
dependencies. [Per Unneberg]
- * rules/bio/ngs/align/star.rules: remove summary plot rule *
rules/bio/ngs/qc/picard.rules: ditto * rules/bio/ngs/qc/rseqc.rules:
ditto * workflows/bio/scrnaseq.workflow: comment out rseqc, star
plots. [Per Unneberg]
- * setup.py: add git dependency to bokehutils. [Per Unneberg]
- Remove snakemakelib.bokeh, update scrnaseq summary output. [Per
Unneberg]
* snakemakelib/bio/ngs/align/star.py: remove snakemakelib.bokeh dependency
* snakemakelib/bio/ngs/qc/rseqc.py: ditto
* snakemakelib/bio/ngs/tests/test_qualimap.py: add duplicated reads
* snakemakelib/bio/ngs/tests/test_star.py: take into account added columns
* snakemakelib/workflow/scrnaseq.py: add plot
* workflows/bio/scrnaseq.workflow: update reporting
- Add more plots for scrnaseq. [Per Unneberg]
* snakemakelib/bio/ngs/qc/rseqc.py: update save function
* snakemakelib/bio/ngs/align/star.py: ditto
* workflows/bio/scrnaseq.workflow: add plots
- Make ATAC-seq reports compatible with bokehutils. [Per Unneberg]
* snakemakelib/bio/ngs/qc/picard.py: finalize compatibility with bokehutils
* snakemakelib/bio/ngs/qc/qualimap.py: add abline, beautify facet plot
- Add bigwig support. [Per Unneberg]
* rules/bio/ngs/db/ucsc.rules: add bigwig support functions
* rules/bio/ngs/enrichment/dfilter.rules: add wig output as default
* rules/bio/ngs/enrichment/macs.rules: add bedgraph output as default
* rules/bio/ngs/enrichment/zinba.rules: add hack to convert bed to
bedgraph (NB: not sure if this is correct)
* rules/comp/settings.rules: add ampersand to source construct
* snakemakelib/bio/ngs/utils.py: PEP8 formatting
* workflows/bio/ATAC-seq.workflow: add bigwig rule
- Add rules to generate bigwig from bed. [Per Unneberg]
* rules/bio/ngs/db/ucsc.rules: add chromsize and bigwig rules
- Start adding support for picard bokehutils. [Per Unneberg]
* snakemakelib/bio/ngs/qc/picard.py: modify parameter sets
- Add bokehutils to qualimap plots. [Per Unneberg]
- Add bokehutils support for cutadapt. [Per Unneberg]
* requirements.txt: add bokehutils
- Update alphas. [Per Unneberg]
* snakemakelib/bio/ngs/qc/qualimap.py: update alpha
* snakemakelib/bokeh/plot.py: ditto
- * snakemakelib/bio/ngs/qc/qualimap.py: add changes *
snakemakelib/bio/ngs/qc/rseqc.py: ditto *
snakemakelib/bio/ngs/regexp.py: ditto *
snakemakelib/bio/ngs/tests/test_star.py: ditto *
snakemakelib/bokeh/plot.py: ditto * templates/star.html: ditto *
templates/workflow_scrnaseq_qc.html: ditto. [Per Unneberg]
- Scatterplot improvements. [Per Unneberg]
* snakemakelib/bio/ngs/align/star.py: add make_scatterplot
* snakemakelib/bio/ngs/qc/qualimap.py: set default intercept
* snakemakelib/bio/ngs/qc/rseqc.py: PEP8 formatting
* snakemakelib/bio/ngs/regexp.py: PEP8 formatting
* snakemakelib/bio/ngs/tests/test_star.py: remove obsolete imports
* snakemakelib/bokeh/plot.py: add abline, data_fields functions
* templates/star.html: check for none table
* templates/workflow_scrnaseq_qc.html: ditto
- * rules/bio/ngs/align/star.rules: make result collection depend on the
right output files. [Per Unneberg]
- Update star reporting utilities. [Per Unneberg]
* snakemakelib/bio/ngs/align/star.py: PEP8 formatting
* snakemakelib/bio/ngs/tests/test_star.py: add star parsing test
* snakemakelib/bokeh/plot.py: remove obsolete plots
* rules/bio/ngs/align/star.rules: use Star parser class
- * snakemakelib/bio/ngs/qc/picard.py: Only share x range. [Per
Unneberg]
- Remove comments. [Per Unneberg]
* templates/picard.html: remove comments
* templates/workflow_atacseq_qc.html: ditto
- Update plotting facilities. [Per Unneberg]
* snakemakelib/bio/ngs/qc/picard.py: add gridplot, make all plots return lists
* snakemakelib/bio/ngs/qc/qualimap.py: kwtext -> text
* snakemakelib/bokeh/plot.py: add make_scatterplot
* snakemakelib/bokeh/publish.py: PEP8 formatting
* templates/cutadapt.html: add jinja2 mode
* templates/picard.html: add rubric
* templates/workflow_atacseq_qc.html: add comments
* workflows/bio/ATAC-seq.workflow: add default qcrules
- Fix failing test. [Per Unneberg]
* snakemakelib/bio/ngs/qc/qualimap.py: add try/except clause
* snakemakelib/bio/ngs/tests/test_qualimap.py: remove qm
* snakemakelib/bokeh/plot.py: make qc dict
- Refactor some ATAC-seq plots. [Per Unneberg]
* rules/bio/ngs/qc/picard.rules: PEP8 formatting
* snakemakelib/bio/ngs/qc/cutadapt.py: PEP8 formatting, use make_dotplot
* snakemakelib/bio/ngs/qc/picard.py: beautify plots
* snakemakelib/bio/ngs/qc/qualimap.py: ditto
* snakemakelib/bokeh/plot.py: update docs, better handling of legend
* templates/qualimap.html: update docs
* workflows/bio/ATAC-seq.workflow: add qualimap to pipeline
- Add qualimap to ATAC-seq workflow. [Per Unneberg]
* rules/bio/ngs/qc/qualimap.rules: do conditional search depending on
whether target starts with run or sample
* templates/qualimap.html: finish standalone html
* templates/workflow_atacseq_qc.html: add qualimap section
* workflows/bio/ATAC-seq.workflow: add qualimap
- Fix globals plot. [Per Unneberg]
* snakemakelib/bio/ngs/qc/qualimap.py: fix parameters to globals plot
* snakemakelib/bio/ngs/tests/test_qualimap.py: refactor test order
* snakemakelib/bokeh/plot.py: revamp make_dotplot to also return
relative plot if desired
* snakemakelib/results.py: make _inputfiles, _samples instance variables
- Add make_dotplot function. [Per Unneberg]
* rules/bio/ngs/qc/qualimap.rules: add qmglobals
* snakemakelib/bio/ngs/qc/qualimap.py: use make_dotplot
* snakemakelib/bio/ngs/tests/test_qualimap.py: add test for globals
* snakemakelib/bokeh/plot.py: add make_dotplot, PEP8 formatting
* snakemakelib/results.py: PEP8 formatting
- Add make_gridplot. [Per Unneberg]
* rules/bio/ngs/qc/qualimap.rules: PEP8 formatting
* snakemakelib/bio/ngs/qc/qualimap.py: add call to make_gridplot
* snakemakelib/bokeh/plot.py: add make_gridplot
- Add sample parsing to results class. [Per Unneberg]
* rules/bio/ngs/qc/qualimap.rules: move sample parsing to Qualimap
* snakemakelib/bio/ngs/tests/test_qualimap.py: PEP8 formatting
* snakemakelib/results.py: add _set_samples
* snakemakelib/tests/test_results.py: add test for sample parsing, PEP8 formatting
- Automated documentation update. [Per Unneberg]
- PEP8 formatting and code cleanup. [Per Unneberg]
- Unset DISPLAY for qualimap. [Per Unneberg]
* rules/bio/ngs/qc/qualimap.rules: unset DISPLAY, add java_mem
* rules/bio/ngs/settings.rules: set java_mem default to 8g
- Add api docs. [Per Unneberg]
- * templates/qualimap.html: add * rules/bio/ngs/qc/qualimap.rules: add
result collection and plotting rules *
snakemakelib/bio/ngs/qc/qualimap.py: add plotting function *
snakemakelib/results.py: filter empty lines. [Per Unneberg]
- * snakemakelib/bio/ngs/qc/qualimap.py: add data parsing *
snakemakelib/bio/ngs/tests/test_qualimap.py: update tests *
snakemakelib/results.py: add load_lines, split functionality *
snakemakelib/tests/test_results.py: set class variable _keys. [Per
Unneberg]
- * rules/bio/ngs/qc/qualimap.rules: add initial support *
snakemakelib/bio/ngs/qc/qualimap.py: add basic result parsing *
snakemakelib/bio/ngs/tests/test_qualimap.py: add basic tests *
snakemakelib/exceptions.py: add exceptions * snakemakelib/results.py:
add generic class for parsing and containing results *
snakemakelib/tests/test_results.py: add basic tests *
snakemakelib/utils.py: add function to set command. [Per Unneberg]
- Completely refactor test directory structure. [Per Unneberg]
Now all tests live in subdirectories to the modules they are supposed
to test.
- Update title and doc ref. [Per Unneberg]
* Readme.md: point docs to rtd
* sphinx/source/index.rst: update title
- Update documentation to comply with sphinx formatting. [Per Unneberg]
* snakemakelib/config.py: update types in docstring
* sphinx/source/conf.py: point to python3.4 by default
* sphinx/source/docs/about.rst: fix code blocks
* sphinx/source/docs/configuration.rst: ditto
* sphinx/source/docs/troubleshooting.rst: add title
* sphinx/source/docs/tutorial.rst: fix code blocks
* sphinx/source/docs/workflows.rst: fix titles and image links
* sphinx/source/index.rst: refactor index
- Add sphinx documentation. [Per Unneberg]
- Update sphinx settings. [Per Unneberg]
* requirements.txt: require sphinx 1.3
* rules/bio/ngs/settings.rules: add global settings
* snakemakelib/rules.py: add input rule modification
* sphinx/source/conf.py: add napoleon extension for Google-style docstrings
- Add support for programmatic rule inheritance. [Per Unneberg]
- * test/test_db_config.py: fix failing test due to updated bwa
reference return vaue. [Per Unneberg]
- * rules/bio/ngs/align/bwa.rules: remove reference to label. [Per
Unneberg]
- * rules/bio/ngs/align/bowtie.rules: update input for bowtie_build2 *
rules/bio/ngs/align/bwa.rules: add indexing rules *
snakemakelib/bio/ngs/db.py: return full ref name for bwa. [Per
Unneberg]
- * rules/bio/ngs/chromatin/danpos.rules: tentatively add dpos rule *
static/basic.css: add table-version * templates/snakemake.html: modify
version style * templates/workflow_scrnaseq_qc.html: move workflow
after snakemake * workflows/bio/ATAC-seq.workflow: add danpos. [Per
Unneberg]
- Add snakemake html template. [Per Unneberg]
- * rules/bio/ngs/chromatin/danpos.rules: add danpos. [Per Unneberg]
- * rules/bio/ngs/align/star.rules: update annotation call *
rules/bio/ngs/db/cloudbiolinux.rules: ditto *
rules/bio/ngs/db/ucsc.rules: add refFlat rule *
rules/bio/ngs/rnaseq/rpkmforgenes.rules: use absolute path for program
call, update annotation * rules/bio/ngs/rnaseq/rsem.rules: update
annotation call * snakemakelib/bio/ngs/db.py: update annotation
function. [Per Unneberg]
- * Readme.md: add branch-specific coverage badges. [Per Unneberg]
- * .travis.yml: use arbitrary caching method. [Per Unneberg]
- * Readme.md: add coverage to table. [Per Unneberg]
- * .travis.yml: add coveralls * Readme.md: add coverall badge. [Per
Unneberg]
- * rules/settings.rules: add _version to global configuration. [Per
Unneberg]
0.0.1 (2015-05-19)
------------------
- * requirements.txt: remove version check for bokeh since it fails for
some reason. [Per Unneberg]
- * setup.py: fix typo. [Per Unneberg]
- Add versioneer. [Per Unneberg]
* setup.py: update to accomodate versioneer
- * Readme.md: add develop and master tags. [Per Unneberg]
- * .travis.yml: add develop to test. [Per Unneberg]
- * Readme.md: add quickstart. [Per Unneberg]
- * .travis.yml: cache pip * data/genomes/Hsapiens/hg19/bowtie/chr11.fa:
add link * data/genomes/Hsapiens/hg19/bwa/chr11.fa: ditto * setup.cfg:
add nosetests section * test/__init__.py: remove obsolete code *
test/test_metrics.py: fix paths * test/test_workflow.py: ditto. [Per
Unneberg]
- * workflows/bio/variation.workflow: flakify and remove filter_suffix *
setup.cfg: add flake8 * .travis.yml: upgrade pip. [Per Unneberg]
- * test/__init__.py: only keep linking to bwa and bowtie * .travis.yml:
add feature branch. [Per Unneberg]
- * rules/bio/ngs/tools/multo.rules: update to working command. [Per
Unneberg]
- * rules/bio/ngs/qc/cutadapt.rules: add log file to output. [Per
Unneberg]
- * rules/bio/ngs/tools/sratools.rules: don't create output file if
user_email is missing. [Per Unneberg]
- * snakemakelib/config.py: add overwrite parameter to overwrite
configuration. [Per Unneberg]
- * snakemakelib/config.py: bug fix: load_sml_config now updates the
config object, regardless if anything already has been set. This
allows for overriding site-wide configuration settings. [Per Unneberg]
- * requirements.txt: add bokeh. [Per Unneberg]
- * setup.py: install data. [Per Unneberg]
- * rules/bio/ngs/tools/sratools.rules: fix link rule *
workflows/bio/scrnaseq.workflow: add quantification config. [Per
Unneberg]
- * rules/bio/ngs/rnaseq/rpkmforgenes.rules: update rules to use unique
and annotation flags * rules/bio/ngs/tools/multo.rules: remove abspath
to home. [Per Unneberg]
- * rules/bio/ngs/enrichment/macs.rules: unclear what files are actually
produced; remove uncertainties * workflows/bio/ATAC-seq.workflow:
update MACS2 output to file that most certainly will be generated?
[Per Unneberg]
- * rules/bio/ngs/align/star.rules: read file in module, remove
filter_suffix * rules/bio/ngs/qc/rseqc.rules: ditto *
rules/bio/ngs/rnaseq/rsem.rules: ditto *
snakemakelib/bio/ngs/align/star.py: read summary file *
snakemakelib/bio/ngs/qc/rseqc.py: ditto * snakemakelib/bokeh/plot.py:
add axis_types to fig members * snakemakelib/utils.py: add
smltemplateenv * templates/rseqc.html: simplify template *
templates/workflow.html: add target *
templates/workflow_scrnaseq_qc.html: modify template to comply with
new config * workflows/bio/scrnaseq.workflow: beautification and
update report. [Per Unneberg]
- * templates/picard.html: beautify * templates/workflow.html: ditto *
templates/workflow_atacseq_qc.html: ditto *
templates/workflow_scrnaseq_qc.html: ditto * workflows/bio/ATAC-
seq.workflow: add report targets * snakemakelib/bio/ngs/qc/picard.py:
improve plotting functions * snakemakelib/bokeh/plot.py: add axes
annotation to lineplot. [Per Unneberg]
- * rules/bio/ngs/qc/cutadapt.rules: remove trailing filter_suffix *
rules/bio/ngs/qc/picard.rules: ditto * setup.py: add templates *
snakemakelib/bio/ngs/qc/cutadapt.py: process file locally and add
data_uri * snakemakelib/bio/ngs/qc/picard.py: add data_uri *
snakemakelib/bokeh/publish.py: fix typo * workflows/bio/ATAC-
seq.workflow: add report rule. [Per Unneberg]
- * rules/bio/ngs/db/ucsc.rules: add home, correct index function call *
rules/bio/ngs/enrichment/zinba.rules: fix ref key *
rules/bio/ngs/qc/picard.rules: remove filter suffix *
rules/bio/ngs/rnaseq/rsem.rules: add dependency on annotation *
rules/bio/ngs/settings.rules: add filter_suffix *
rules/bio/ngs/tools/bamtools.rules: add home *
rules/bio/ngs/tools/bedtools.rules: update name * rules/utils.rules:
update rulegraph output names * snakemakelib/config.py: update debug
message * snakemakelib/stat.py: add default compression suffixes *
workflows/bio/ATAC-seq.workflow: update to comply with new
configuration, make include statements conditional on peakcallers,
beautification of targets. [Per Unneberg]
- * wiki: update. [Per Unneberg]
- * test/bio/ngs/tools/test_sratools.py: update test to comply with new
config routines * test/test_config.py: ditto * test/test_db_config.py:
ditto * test/test_workflow.py: ditto *
rules/bio/ngs/align/bowtie.rules: add home *
rules/bio/ngs/align/bwa.rules: correct ref *
rules/bio/ngs/align/star.rules: add log *
rules/bio/ngs/db/cloudbiolinux.rules: use fasta in extra_ref *
rules/bio/ngs/db/ercc.rules: write fasta and genbank *
rules/bio/ngs/rnaseq/rsem.rules: add bowtie path *
rules/bio/ngs/settings.rules: update ref *
rules/bio/ngs/tools/sratools.rules: add log *
snakemakelib/bio/ngs/db.py: remove index2 *
snakemakelib/bio/ngs/tools/sratools.py: exception only *
snakemakelib/config.py: require config parameter for load_sml_config.
[Per Unneberg]
- Update config usage. [Per Unneberg]
- * rules/bio/ngs/align/star.rules: update config usage, make indexing
depend on input gtf * rules/bio/ngs/db/ucsc.rules: update config
usage, add genepred rule, add rule for generating pipeline-ready
reference * rules/bio/ngs/qc/rseqc.rules: update config usage *
rules/bio/ngs/rnaseq/rpkmforgenes.rules: ditto *
rules/bio/ngs/rnaseq/rsem.rules: ditto, update index function *
rules/bio/ngs/settings.rules: set default gtf, add extra_ref *
rules/bio/ngs/tools/bamtools.rules: update config usage *
rules/bio/ngs/tools/bedtools.rules: ditto *
rules/bio/ngs/tools/conversion.rules: ditto *
rules/bio/ngs/tools/sratools.rules: ditto, also merge info and
biosample output * rules/settings.rules: add protected file types *
snakemakelib/bio/ngs/db.py: refactor index, ref functions, add
annotation * snakemakelib/bio/ngs/tools/sratools.py: fix parameters *
snakemakelib/config.py: make load_sml_config be a required rule *
snakemakelib/io.py: add support for protected rules *
snakemakelib/log.py: warn if we try to get existing logger *
snakemakelib/stat.py: remove direct dependency on config *
workflows/bio/ATAC-seq.workflow: add set_output *
workflows/bio/scrnaseq.workflow: ditto, and update config usage. [Per
Unneberg]
- Replace update_sml_config with update_snakemake_config and the like at
relevant positions. [Per Unneberg]
- * rules/settings.rules: add protected settings * snakemakelib/io.py:
update output function to take into account both temporary and
protected output * workflows/bio/ATAC-seq.workflow: use new set_output
function * workflows/bio/scrnaseq.workflow: ditto. [Per Unneberg]
- * rules/bio/ngs/enrichment/macs.rules: add log * workflows/bio/ATAC-
seq.workflow: correct macs2 options. [Per Unneberg]
- * rules/bio/ngs/tools/sratools.rules: add restraint on SRR fastq name.
[Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: add log output *
rules/bio/ngs/tools/sratools.rules: fix fastq link rule *
rules/settings.rules: add sra filetype * snakemakelib/io.py: add
warning message if no outputs set to temp * workflows/bio/ATAC-
seq.workflow: update macs options. [Per Unneberg]
- * rules/bio/ngs/enrichment/dfilter.rules: add PATH *
rules/bio/ngs/qc/cutadapt.rules: add uris *
rules/bio/ngs/qc/picard.rules: output csv, add uri *
snakemakelib/bio/ngs/qc/cutadapt.py: pass data frame *
snakemakelib/bio/ngs/qc/picard.py: fix percent columns, beautify plot
call * snakemakelib/bio/ngs/qc/rseqc.py: beatify plot calls *
snakemakelib/bokeh/plot.py: add scatterplot2 * workflows/bio/ATAC-
seq.workflow: add align targets. [Per Unneberg]
- * rules/bio/ngs/qc/cutadapt.rules: update data summary rules *
snakemakelib/bokeh/plot.py: add dotplot. [Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: add benchmark *
rules/bio/ngs/qc/picard.rules: add template *
snakemakelib/bio/ngs/qc/picard.py: add metrics plotting utilities *
snakemakelib/bokeh/plot.py: add lineplot *
snakemakelib/bokeh/publish.py: do recursive update of template
keywords * workflows/bio/ATAC-seq.workflow: add cutadapt execution.
[Per Unneberg]
- * rules/bio/ngs/tools/bamtools.rules: add installation check *
rules/bio/ngs/tools/bedtools.rules: readd home. [Per Unneberg]
- * snakemakelib/bio/ngs/align/star.py: use new plotting interface in
snakemakelib.bokeh.plot * snakemakelib/bio/ngs/qc/rseqc.py: ditto *
snakemakelib/bokeh/plot.py: new. [Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: parametrize bowtie *
rules/bio/ngs/enrichment/macs.rules: update macs rule *
rules/bio/ngs/qc/cutadapt.rules: move from sequenceprocessing *
rules/bio/ngs/qc/picard.rules: add qc rules *
rules/bio/ngs/qc/sequenceprocessing.rules: remove cutadapt *
rules/bio/ngs/tools/sratools.rules: fix conflicting rules *
snakemakelib/io.py: require input to set_temp_output * workflows/bio
/ATAC-seq.workflow: add options * workflows/bio/scrnaseq.workflow: fix
temp_output. [Per Unneberg]
- * snakemakelib/bio/ngs/tools/sratools.py: update error message on
analysis startup. [Per Unneberg]
- * wiki: update. [Per Unneberg]
- * rules/bio/ngs/enrichment/dfilter.rules: correct parameter string *
rules/bio/ngs/enrichment/zinba.rules: reorganize configuration dict *
rules/bio/ngs/motif/gem.rules: add installation info * workflows/bio
/ATAC-seq.workflow: add information about additional analyses *
workflows/bio/scrnaseq.workflow: add bamtools_filter to
temp_rules_default. [Per Unneberg]
- * snakemakelib/bio/ngs/utils.py: add function to convert dict to
R-compatible dict. [Per Unneberg]
- * rules/bio/ngs/enrichment/zinba.rules: add run.zinba rule. [Per
Unneberg]
- * rules/bio/ngs/enrichment/dfilter.rules: add dfilter support *
rules/bio/ngs/enrichment/zinba.rules: correct output file names *
rules/bio/ngs/rnaseq/rsem.rules: remove bam output *
rules/bio/ngs/tools/sratools.rules: add title to biosample output *
templates/workflow_scrnaseq_qc.html: add rulegraph * workflows/bio
/ATAC-seq.workflow: rewrite ruleorders *
workflows/bio/scrnaseq.workflow: add temp_rules, add report output.
[Per Unneberg]
- * rules/settings.rules: use temp_filetypes_default *
snakemakelib/io.py: ditto * rules/utils.rules: add rules to generate
rulegraph plot and configuration output. [Per Unneberg]
- * rules/bio/ngs/enrichment/zinba.rules: update alignability target *
rules/bio/ngs/rnaseq/rsem.rules: add installation check *
rules/bio/ngs/tools/sratools.rules: add logger * workflows/bio/ATAC-
seq.workflow: update alignability target *
workflows/bio/scrnaseq.workflow: add qc and pca rule. [Per Unneberg]
- * rules/bio/ngs/tools/sratools.rules: add rule to download phenotype
data. [Per Unneberg]
- * rules/bio/ngs/align/blat.rules: remove duplicate link rule *
rules/bio/ngs/db/ucsc.rules: make ucsc_write_chromosome write output
files prefixed with 'chr' [Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: update check for program *
rules/bio/ngs/tools/bedtools.rules: ditto. [Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: update align and index commands *
rules/bio/ngs/db/ucsc.rules: add several rules to generate custom
references * rules/bio/ngs/enrichment/peakseq.rules: remove obsolete
rules and simplify names * rules/bio/ngs/enrichment/zinba.rules: add
putatively working functions * rules/bio/ngs/qc/picard.rules: add dict
rule * rules/bio/ngs/tools/bedtools.rules: remove obsolete home *
snakemakelib/io.py: extend default temp files * workflows/bio/ATAC-
seq.workflow: add correction rule. [Per Unneberg]
- * requirements.txt: add pysam * rules/bio/ngs/align/bowtie.rules: fix
bowtie aligment rule * rules/bio/ngs/enrichment/peakseq.rules: add
docstring * rules/bio/ngs/qc/picard.rules: merge: do copy instead of
symlink * rules/settings.rules: add temp_files * snakemakelib/io.py:
only include large file types in temp_files. [Per Unneberg]
- * rules/bio/ngs/enrichment/peakseq.rules: add rules for generating
mappability files. [Per Unneberg]
- * rules/bio/ngs/enrichment/peakseq.rules: add. [Per Unneberg]
- * requirements.txt: add biopython *
rules/bio/ngs/enrichment/zinba.rules: add peakseq, clean up rules *
rules/bio/ngs/qc/picard.rules: improve find_merge_inputs *
rules/bio/ngs/settings.rules: add read_length *
rules/bio/ngs/tools/sratools.rules: add log *
snakemakelib/bio/ngs/db.py: add chromosomes *
snakemakelib/bio/ngs/regexp.py: add __repr__ * snakemakelib/utils.py:
add safe_makedir * workflows/bio/ATAC-seq.workflow: update suffix.
[Per Unneberg]
- Remove obsolete code. [Per Unneberg]
- * rules/settings.rules: add temp_rules configuration parameter *
snakemakelib/io.py: add set_temp_output * workflows/bio/ATAC-
seq.workflow: add temp_output. [Per Unneberg]
- * rules/bio/ngs/enrichment/macs.rules: add. [Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: fix readgroup error *
workflows/bio/ATAC-seq.workflow: fix ruleorders. [Per Unneberg]
- * rules/bio/ngs/chipseq/macs.rules: add macs rules. [Per Unneberg]
- * rules/bio/ngs/motif/gem.rules: add. [Per Unneberg]
- * rules/bio/ngs/align/bowtie.rules: add bowtie rules outside tuxedo *
rules/bio/ngs/enrichment/zinba.rules: modify options, add template *
rules/bio/ngs/methylseq/rnbeads.rules: move dict_to_R to
snakemake.bio.ngs.utils * rules/bio/ngs/qc/picard.rules: unlink file
if symlink to be done on force * rules/bio/ngs/rnaseq/tuxedo.rules:
update index calls * snakemakelib/bio/ngs/utils.py: add dict_to_R *
workflows/bio/ATAC-seq.workflow: add initial configurations. [Per
Unneberg]
- * workflows/bio/ATAC-seq.workflow: Add. [Per Unneberg]
- * rules/bio/ngs/methylseq/rnbeads.rules: add ngs_cfg. [Per Unneberg]
- * rules/bio/ngs/methylseq/rnbeads.rules: update rnbeads run rule. [Per
Unneberg]
- * rules/bio/ngs/methylseq/rnbeads.rules: update analysis from bed.
[Per Unneberg]
- * rules/bio/ngs/methylseq/rnbeads.rules: Add rnbeads rules *
rules/utils.rules: Need sml_rules_path. [Per Unneberg]
- * rules/bio/ngs/db/ucsc.rules: add rules for dealing with ucsc data,
mainly downloads * rules/bio/ngs/enrichment/zinba.rules: add rules for
zinba. [Per Unneberg]
- * snakemakelib/log.py: fix setting log from config. [Per Unneberg]
- * wiki: [Per Unneberg]
- * wiki: [Per Unneberg]
- * rules/bio/ngs/tools/samtools.rules: remove obsolete rule *
rules/utils.rules: ditto * setup.py: remove obsolete info; add
examples * wiki: updated. [Per Unneberg]
- * wiki: update. [Per Unneberg]
- * rules/bio/ngs/rnaseq/rsem.rules: save dataframe as csv *
workflows/bio/scrnaseq.workflow: add qc section. [Per Unneberg]
- * requirements.txt: add scikit, statsmodels *
rules/bio/ngs/qc/picard.rules: remove bam_bai rule *
rules/bio/ngs/qc/rseqc.rules: finish up summary rules *
rules/bio/ngs/rnaseq/rsem.rules: add parsing of rsem result files *
snakemakelib/bio/ngs/align/star.py: add brewer colors *
snakemakelib/bio/ngs/qc/rseqc.py: finish up summary functions *
workflows/bio/scrnaseq.workflow: remove obsolete rule_order. [Per
Unneberg]