ChangeLog

CHANGES
=======

* split up zebrafish contamination into mito - rrna - zebrafish
* or it wasn't found on fexList // let's just omit info, code is the doc (?)
* autoreformatted for flake8 rule
* fixes
* works in my server :P
* FutureWarning: Calling int on a single element Series is deprecated and will raise a TypeError in the future
* flake8 fix
* URL should be complete
* use 1 config param (URL) instead of 3
* flake8 E302
* get\_contact\_details API endpoint // deprecated userList text file
* Lanesplit samples (#173)
* make lanesplit check on sampleIDs rather then samplenames, and lane aware
* Mycoplasma implement, email update (#172)
* Contam emails (#171)
* ChangeLog
* actual seq\_data dir in email
* mycoplasma include in prep
* include mycoplasma hyorhinis
* docs updates (#170)
* auto version for docs, fix readthedocs yaml (#169)
* auto version for docs, fix readthedocs yaml
* Docs (#168)
* update changelog
* include authors
* make sure doc pytest includes reqs from the doc folder
* init readthedocs yaml, split up doc requirements
* seq\_data dirs & docs (#166)
* Allow new seq dirs when older are not full yet. (#165)
* Allow new seq dirs when older are not full yet
* adding documentation for certificate change problems (#162)
* Main (#164)
* force listing of PIdirs to be sorted (#163)
* force listing of PIdirs to be sorted
* Update usage.rst
* updating certificate issue
* adding documentation for certificate change problems

v0.2.6
------

* Main (#159)
* Dev wd (#158)
* include 20 in comment as well
* miseq reqdepth override to 20
* flake
* move reqdepth change in classes due to parkour returning everything
* santize sample names (space in names)
* software version to debug log in main func
* Main (#157)
* Fix148 ks (#156)
* flake fix
* cleanup
* gitignore
* added ulautDestroyer to sampleSheetClass parser
* fix #153 (#154)
* bumped pandas version in env.yml
* attempted to fix the pandas error
* Main (#152)
* old GH action was deprecated
* Fix #148 (#149)
* accent fixes in umlautDestroyer

v0.2.5
------

* MiSeq (#146)
* bugfix rerun w/ existing samplesheet (P5RC flag missing if no .bak)
* escape validation w/ novaseq
* follow new seqfac structure
* CompletionStatus check and initiation of failedrun
* include kraken explanation from ini file in mqc as feature
* fly rename contam

v0.2.4
------

* purge apostrofs
* flake minor formatting
* update email with some red
* automated P5 RC in Miseqs run if all samples are empty
* purge apostrofs
* flake minor formatting
* update email with some red
* automated P5 RC in Miseqs run if all samples are empty
* purge apostrofs
* flake minor formatting
* update email with some red
* automated P5 RC in Miseqs run if all samples are empty

v0.2.3
------

* sometimes projects are omitted from a flow cell (budgetary regions). Escape Nonetypes in the mqc building
* escape nones in libtypes
* include non-ommitted empty samples in kraken for email
* flake fix/precommit version boost
* Finalize omit samples in email. Only display project exitstats of that specific lane
* flake fix/precommit version boost
* Finalize omit samples in email. Only display project exitstats of that specific lane
* colliding samples that are removed from a demuxsheet cause issues in postmux stage. This commit escapes those
* flake8 demux
* simplify the substr check
* changing scATAC protocols in parkour
* bugfix fex bool parse
* bugfix fex bool parse

v0.2.2
------

* bugfixes (#127)
* Wd (#125)
* Wd (#124)
* Wd (#122)

v0.2.1
------

* tests & empty report fix (#120) (#121)
* WIP - fixes (#119)

v0.2.0
------

* Wd (#113) (#114)
* Wd (#113)
* include abs gotten reads, bugfix with parkourOrg in empty samples (#111)
* logging a mode + force config
* log restructuring
* fq file ending check + regex soup
* fq file ending check
* exit email when project folder doesnt exist
* split up ercc & vectors
* make sure sampleID is set before entering try/except block (#100)
* make sure sampleID is set before entering try/except block
* Precommit (#96)
* include prod in tests (#95)
* detmask (#94)
* Fix no index (#92)
* Wd (#88)
* flake fix
* add a check group check for all files in wd40 rel
* Docs (#87)
* left join only include samples in origin ss / demuxsheet
* Docs (#83)
* executables docs
* ixdepth1 config.ini explanation
* Wd (#80)
* flake
* purge print kraken reps, include diskspace per transferred project
* broken link aeae28S
* flake fixes
* contaminome mosquito&drosC
* Wd (#79)
* include 10xscATAC case
* Wd (#76)
* reload setlog, escape empty kraken reports, flake
* move over sleeper
* fly to drosophila in contaminome
* Wd (#74)
* purge fq screen in conf, mentions etc
* kraken (#73)
* shift to kraken
* Wd (#72)
* update env name in tests
* strip name from env
* quickload config, badges
* fix badges
* badges
* rtfd (#71)
* merge
* add rtfd link, slight update docs

v0.1.1
------

* executables&docs (#70)
* env fix
* release syntax
* merge include wd40 rel
* Initiate kraken build contaminome db. purge most executables and ship into conda env initiate docs
* fixed bug with Cc and transfered bioinfo\_cc to Bcc
* transfered hardcoded filenames and signatures to ini-file
* fixed flake8 issues
* added cc to bioinfo-core
* added src/tools to include emailProjectFinished.py
* minor wd40 changes
* flake
* init diag
* include wd40 in repo
* sys exits accompanied by error emails
* flake
* add version to email now as well
* parse fexsend l newline
* switch to mamba
* fex cmds to log
* get rid of dev exit
* update mask/dualIx/overwritten barcodes
* force writing a demuxSheet that can be manipulated with mixed single-dual index runs
* Update misc.py
* strip wd env
* include version upon invocation
* flake fix
* strip print clutter
* rebase Merge branch 'main' of github.com:maxplanck-ie/dissectBCL into WD
* move reqs to conda, purge dissect\_test, add args

v0.1.0
------

* versioning in mqc is done
* fix the version used in project reports
* strip some CICD
* strip conf read test from tests for now
* try abspath for env act
* rename env.yml
* mambo nr 5
* split up step
* drop double uses
* add checkout action
* conda fix actions
* try conda tests
* flake fix misc
* cap flake8
* revert flake to pip install alone
* change flake to conda build
* switch build conda
* add certs for API requests. Choose key depending on test vs prod run
* fix flake
* specify cert for requests
* remove bin folder switch from setup.py to setup.cfg specify entry points in setup cfg specify regular and test entry points
* retain log.warning rather than log.info for easier readability
* replaced np.isnan with pandas.isna
* added branch manke to pytest.yml
* added checks to postmux:matchIDtoName
* potential bugfix pp?
* add interOp parsing to report back reads PF
* flake8 fix
* additional check lanesplit for clashing samples
* change from pd.Series to dict in sampleID accession
* purge flake8 file / update gitignore
* free py minor fixes
* FIX sampleID not found @ 220620\_M\*\_1
* flake fix
* bugfix duplicated sampleNames
* remove fPath main fun
* babysteps on API walk
* Less checks, more patches 🙈
* parkour parsing
* minor bugfix for projects with a space, and descrptions with \\`
* flake fix
* fix parkour pushes for MiSeq runs
* print out hammings for now
* purge space in projects
* bugfix minP5 in general mask, strip except email
* email on crash

v0.0.2
------

* get rid of PE vs SE in requested (assuming requested is allways fragments)
* mqc enhancements
* flake pass
* add in sampleID to email, bugfix R1\_perc Q30 in non-lane split flowcells
* bugfix nonlanesplit

v0.0.1
------

* pycov req
* crash on parkour failure
* flake
* small changes
* pytest update retBC/retIX
* flake fix
* minor bug fixes, add md5sum
* flake testing
* pytest updates
* getting started with datafiles
* pytest change
* workflows update
* start testing
* Update tests Merge branch 'WD' of github.com:maxplanck-ie/dissectBCL into WD
* work on tests
* postmux fin
* force ints mask
* greeter & scATAC demux
* flake, omit some debugs
* tiny bugfix parsing email/drHouse
* fex & finalisation
* flake
* parkour push implement
* make sure we dont reprocess bfq.py
* implement sleeper
* classes flake
* flake fakenews
* postmux flake
* misc flake
* houseFlake
* demux flake
* functioning seqreport in multiqc
* start config to add requested column in general stats
* remove seqrep funcs, add multiqc yaml parser
* remove seqrep funcs, introduce umlaut destroyer
* remove seqrep from dissect
* start reworking multiqc to omit sequencingreport.pdf
* move from pyyaml to ruamel.yaml for multiqc yaml dumping
* start purging seqRep.pdf
* keep track todo
* logfile reorg
* round of G/R in seqRep
* flake8
* email updates
* dissect ini example
* ignore
* flake finished
* flake drhouse
* remove class returns because of redundancy, add some return strings to make log/debug downstream easier
* drHouse flake
* dissect flake
* flake test misc
* fakenews flaker
* class flake
* finalise email
* email updates&start copy
* bugfix indexType parsing
* multipage seqreps + long sample names
* seqrep splitter
* seqrep updates
* minor bug fixes
* flake fin
* fakenews flaked
* demux flake
* logger flake
* seq report fin
* seq report
* demux flake
* sequencing report updates
* pdf changes and logger
* parse demux stats and update ss class
* update general tex template
* tex templates for PE and SE seq
* rebuilding seq report
* flake fakenews
* init sequencing report
* multiqc
* flake
* qc updates
* init fqc/clump
* fastqc pool running
* fastqc implement
* renaming
* badgetest
* flake test
* add pip install to pytest
* Create pytest.yml
* purge placeholders
* testing hello world
* ignore update for tests
* include test setup
* Update misc.py
* readline
* small bugfix
* test protect
* testrm
* test
* readme update
* loosen python version
* Update flake.yml
* flake python 3.9.2
* Update flake.yml
* Update flake.yml
* Update flake.yml
* Update flake.yml
* Update flake.yml
* Rename flake to flake.yml
* flaketest
* placeholders test
* flaketest
* index2 update
* flake
* demux flake
* fkaenews flake
* flakeDissect
* flakes classes
* cleanup
* flake
* demux
* Up until demuxing
* demuxSheet
* masking updates
* preFQ init
* logger start
* updates
* pops
* updates
* classDefs
* flake8 preFQ
* flake8 dissect.py
* purge egg build
* fq
* purge build
* executable
* gitignore
* flowcell finder
* preFQ start
* gitignore
* remove build
* init
* Initial commit