Recent Releases of porecov
porecov - 1.12.4 Small fix for csv input and filesize filter
What's Changed
- Fix: disable filesize filer with csv input by @MarieLataretu in https://github.com/replikation/poreCov/pull/286
Full Changelog: https://github.com/replikation/poreCov/compare/1.12.3...1.12.4
- Nextflow
Published by replikation 7 months ago
porecov - 1.12.3 Improved stability
What's Changed
- Change get porcov version by @MarieLataretu in https://github.com/replikation/poreCov/pull/285
Full Changelog: https://github.com/replikation/poreCov/compare/1.12.2...1.12.3
- Nextflow
Published by replikation 7 months ago
porecov - 1.12.2 fixing update bug
What's Changed
- fix
VariableNetCheckeralready definederror by @MarieLataretu in https://github.com/replikation/poreCov/pull/284 - pangolin and nextflow container are updated to more recent versions
Full Changelog: https://github.com/replikation/poreCov/compare/1.12.1...1.12.2
- Nextflow
Published by replikation 7 months ago
porecov - 1.12.1 fix on potential bug
Full Changelog: https://github.com/replikation/poreCov/compare/1.12.0...1.12.1
- Nextflow
Published by replikation 7 months ago
porecov - 1.12.0 for nextflow 24.10.4
What's Changed
- Implementation of nextflow strict syntax by @DataSpott in https://github.com/replikation/poreCov/pull/281
- min nextflow version is 24.10.4
- --list is deprecated but "auto" included
- --fastq supports now directly .csv input (previously needed --list)
- --help cleanup
Full Changelog: https://github.com/replikation/poreCov/compare/1.11.2...1.12.0
- Nextflow
Published by replikation 7 months ago
porecov - 1.11.2
What's Changed
- skip removing small fastq.gz files after the length filter with --list or --sample by @MarieLataretu in https://github.com/replikation/poreCov/pull/279
Full Changelog: https://github.com/replikation/poreCov/compare/1.11.1...1.11.2
- Nextflow
Published by MarieLataretu about 1 year ago
porecov - 1.10.0 Freja integration and more
What's Changed
- changed the error strategy in slurm profile by @MarieLataretu in https://github.com/replikation/poreCov/pull/265
- Freyja integration by @DataSpott in https://github.com/replikation/poreCov/pull/268
- added the latest midnight primers (V5.2.0_1200) by @MarieLataretu in https://github.com/replikation/poreCov/pull/269
- Feature add af to vc fs by @MarieLataretu in https://github.com/replikation/poreCov/pull/273
Full Changelog: https://github.com/replikation/poreCov/compare/1.9.4...1.9.5
- Nextflow
Published by replikation over 1 year ago
porecov - 1.9.4
What's Changed
- Feature: add nextclades pango assigment by @MarieLataretu in https://github.com/replikation/poreCov/pull/261
- bump default container version for pangolin and nextclade by @MarieLataretu in https://github.com/replikation/poreCov/pull/264
Full Changelog: https://github.com/replikation/poreCov/compare/1.9.3...1.9.4
- Nextflow
Published by DataSpott about 2 years ago
porecov - slight config adjustments
What's Changed
- added timestamp to reports; solves #256 by @MarieLataretu in https://github.com/replikation/poreCov/pull/257
Full Changelog: https://github.com/replikation/poreCov/compare/1.9.2...1.9.3
- Nextflow
Published by replikation over 2 years ago
porecov - 1.9.0 updates and enhancements
What's Changed
- Update medaka by @MarieLataretu in https://github.com/replikation/poreCov/pull/255
- [Enhancment] publish more logs/intermediate files from ARTIC by @MarieLataretu in https://github.com/replikation/poreCov/pull/252
- [Feature] added parameter artic_normalize by @MarieLataretu in https://github.com/replikation/poreCov/pull/251
Full Changelog: https://github.com/replikation/poreCov/compare/1.8.3...1.9.0
- Nextflow
Published by replikation over 2 years ago
porecov - 1.8.3 bux fix on president docker
What's Changed
- updated president version and docker hub account by @MarieLataretu in https://github.com/replikation/poreCov/pull/253
Full Changelog: https://github.com/replikation/poreCov/compare/1.8.2...1.8.3
- Nextflow
Published by replikation almost 3 years ago
porecov - 1.8.2
What's Changed
- Update medaka in artic by @hoelzer in https://github.com/replikation/poreCov/pull/250
We're using the ARTIC pipeline in version 1.3.0-dev, which had an older medaka installed. In this release, we bump the medaka version to 1.7.2 and support newer models for R10.4.1 flow cells.
Full Changelog: https://github.com/replikation/poreCov/compare/1.8.1...1.8.2
- Nextflow
Published by hoelzer about 3 years ago
porecov - 1.8.0
What's Changed
- [Feature] more info on Ns by @MarieLataretu in https://github.com/replikation/poreCov/pull/243
- bumped predefined LCS table to 2023-01-26 by @MarieLataretu in https://github.com/replikation/poreCov/pull/244
- [Feature] add ARTIC V5 and V5.1 by @MarieLataretu in https://github.com/replikation/poreCov/pull/242
- [Bugfix] correction of VarSkip2b primer-scheme by @DataSpott , solving issue #246
Full Changelog: https://github.com/replikation/poreCov/compare/1.7.2...1.8.0
- Nextflow
Published by DataSpott about 3 years ago
porecov - addition of "VarSkipV2b" primer-set
- addition of "VarSkipV2b" primer-set by @bwlang
Full Changelog: https://github.com/replikation/poreCov/compare/1.7.0...1.7.1
- Nextflow
Published by DataSpott over 3 years ago
porecov - bumping up to nextclade 2
- bumping pangolin min container
- changed code to support nextclade 2 now and included the CLI changes
Full Changelog: https://github.com/replikation/poreCov/compare/1.6.1...1.7.0
- Nextflow
Published by replikation over 3 years ago
porecov - deactivate scorpio by default
- scorpio for lineage is deactivated by default (activate via
--scorpio) as it overwrites some lineage assessments of BA.4 and BA.5
What's Changed
- added skip-scorpio parameter fixes #234 by @MarieLataretu in https://github.com/replikation/poreCov/pull/235
Full Changelog: https://github.com/replikation/poreCov/compare/1.6.0...1.6.1
- Nextflow
Published by replikation over 3 years ago
porecov - 1.6.0 publishing the vcf file and updates for the read lineage screen
What's Changed
- LCS UCSC marker update feature by @MarieLataretu in https://github.com/replikation/poreCov/pull/231
- publish vcf file, fixes #232 by @MarieLataretu in https://github.com/replikation/poreCov/pull/233
Full Changelog: https://github.com/replikation/poreCov/compare/1.5.1...1.6.0
- Nextflow
Published by replikation almost 4 years ago
porecov - 1.5.0
- included the new pangolin version 4 and some minor changes and adjustments
What's Changed
- Pangolin4 update by @RaverJay in https://github.com/replikation/poreCov/pull/224
- Split LCS barplot by @MarieLataretu in https://github.com/replikation/poreCov/pull/225
- other stuff @replikation in https://github.com/replikation/poreCov/pull/228
Full Changelog: https://github.com/replikation/poreCov/compare/1.4.1...1.5.0
- Nextflow
Published by replikation almost 4 years ago
porecov - 1.4.0 include LCS lineage read screening
What's Changed
- included LCS pooled sample implementation by @hoelzer and @replikation in https://github.com/replikation/poreCov/pull/216
- can be activated via
--screen_reads - can take approx. 4-5 h per sample! so make sure you have a cluster/cloud to distribute the workload
- can be activated via
- bumping the default nextclade and pangolin containers
- updated kraken2 database via @oliverdrechsel for read classification closes #178
Full Changelog: https://github.com/replikation/poreCov/compare/1.3.0...1.4.0
- Nextflow
Published by replikation almost 4 years ago
porecov - improved report
What's Changed
Improvements made by @RaverJay to improve the readability of the HTML report * Report VOCs, VOIs in the final report by @RaverJay in https://github.com/replikation/poreCov/pull/206 * Table style updates by @RaverJay in https://github.com/replikation/poreCov/pull/213
Full Changelog: https://github.com/replikation/poreCov/compare/1.2.1...1.3.0
- Nextflow
Published by replikation about 4 years ago
porecov - update on varskip2 primer
What's Changed
- VarskipV2, pool fix and consistent ordering by @bwlang in https://github.com/replikation/poreCov/pull/212
- updated help and readme to better understand how to provide custom primer bed files @replikation
New Contributors
- @bwlang made their first contribution in https://github.com/replikation/poreCov/pull/212
Full Changelog: https://github.com/replikation/poreCov/compare/1.2.0...1.2.1
- Nextflow
Published by replikation about 4 years ago
porecov - 1.2.0
What's Changed
- seqrs V4.1 support and singularity envWhitelist by @MarieLataretu in https://github.com/replikation/poreCov/pull/208
- Custom bed file input by @replikation in https://github.com/replikation/poreCov/pull/211
- provide your own bed files via `
--primerV ownprimerfile.bed- documentation will be added soon for this. make sure your bed file follows the same artic primer rules with naming etc.
- working primer support for VarSkipV2
Full Changelog: https://github.com/replikation/poreCov/compare/1.1.0...1.2.0
- Nextflow
Published by replikation about 4 years ago
porecov - 1.1.0
What's Changed
- adding VarSkip2 primer by @replikation in https://github.com/replikation/poreCov/pull/203
- Report command line by @RaverJay in https://github.com/replikation/poreCov/pull/197
- Bump Medaka version in ARTIC container by @hoelzer in https://github.com/replikation/poreCov/pull/196
- Use nextclade aa insertions by @RaverJay in https://github.com/replikation/poreCov/pull/198
- add frameshift column by @RaverJay in https://github.com/replikation/poreCov/pull/205
- Bump default Pangolin and Nextclade container
Full Changelog: https://github.com/replikation/poreCov/compare/1.0.0...1.1.0
- Nextflow
Published by replikation about 4 years ago
porecov - 1.0.0
- added mid barcode detection, slightly increases overall read number after demultiplexing
- VarSkip primer added
- ARTIC 4.1 primer set added (omicron support)
- disabled guppy pings to avoid errors in some cases
- insertion are now added to the report
- gzip FASTA support
- default pangolin and nextclade container are up. (we still recommend using the
--updateflag for the most recent definitions)
- Nextflow
Published by replikation about 4 years ago
porecov - 0.11.7
Quick fix for reporting amino acid insertions in the report: Nextclade changed the index and thus we needed to adjust the translation of insertions reported on nucleotide level in Nexclade to insertions on amino acid level for the report.
- Nextflow
Published by hoelzer about 4 years ago
porecov - 0.11.4
- add insertions to the report
- this is done currently via translating nt insertions reported by
Nextcladeinto aa insertions to show them in the report, e.g. for Omicron
- this is done currently via translating nt insertions reported by
- add information about
scorpioandscorpio constellationfiles to the report, also put other important tool versions more prominent on top of the report - allow gzip FASTA input
- bumps up default version of
PangolinandNextcladeto new ones
- Nextflow
Published by hoelzer about 4 years ago
porecov - 0.11.3
- first length-filter the input reads and then classify with
kraken2- before, reads were length-filtered but the raw reads were classified with
kraken2, leading to classifications of primer-dimers and other too sort (or too long) reads that are anyway not further used in the following steps of the pipeline
- before, reads were length-filtered but the raw reads were classified with
Attention: If you have for example a high proportion of short reads in your sample that are sorted out be --minLength, their classification as SARS-CoV-2, human or unknown will not reflect them anymore.
- Nextflow
Published by hoelzer over 4 years ago
porecov - small fix to nanopolish output
- small fix to nanopolish output
- Nextflow
Published by replikation over 4 years ago
porecov - 0.11.1 VarSkip primer support
- support added for NEB varskip primer here
- activate via
--primerV VarSkipV1asee also--helpfor all supported schemes - example command:
bash nextflow run replikation/poreCov -r 0.11.1 --fastq_pass fastq_pass/ --primerV VarSkipV1a --update -profile local,docker - default for the amplicon inclusions:
Min read-length set to: 350 [--minLength] Max read-length set to: 700 [--maxLength]
- Nextflow
Published by replikation over 4 years ago
porecov - 0.11.0
Release 0.11.0
polishing models for guppy 5.x
- important guppy (for basecalling) / medaka (for genome polishing) model settings are both set default to high accuracy (hac)
- make sure that you are using the correct models
- if you basecall on a gridion or minion with
hacsettings the default medaka_model is fine if you are using guppy version 5 or higher (make sure to update minknow software)
java
guppy_model = 'dna_r9.4.1_450bps_hac.cfg'
medaka_model = 'r941_min_hac_g507'
* alternatively you could use nanopolish to avoid the whole model stuff (needs the fast5 data for polishing)
Additions and fixes
--updatenow downloads the latest available pangolin AND nextclade container- for both the tool version and the database data are mentioned in the final report
- this ensures that you can run porecov always with the latest available lineage and clade definitions
- for both the tool version and the database data are mentioned in the final report
- fixed some errors by downloading databases via
wget(https certificates) should be now future proof --sampleinput now checks if headers are present and if all fields are present (barcodes and sample names)- Please make sure that you are not using excel to generate the input csv use node pad, text-editor etc., any program that is not introducing strange hidden symbols.
- V4 primer support included (
--primerV V4) - fixed some bugs for CoVarplots
- medaka models for polishing are now pre-downloaded for the container
--min_depthparameter (default 20) added, can be used for low depth genomes ( with only a few reads)- will be bad quality genomes but is usually enough to roughly determine the lineage it is from
- will be bad quality genomes but is usually enough to roughly determine the lineage it is from
- Nextflow
Published by replikation over 4 years ago
porecov - 0.10.1 Add support for all available medaka models
After installation, medaka only comes with a bunch of most recent default models. Further (e.g. older) models are downloaded automatically the first time they are requested which can make issues on systems that have restricted internet access.
- added a new container for the ARTIC pipeline that has pre-downloaded medaka models
- Nextflow
Published by hoelzer over 4 years ago
porecov - guppy 5.x support and min depth parameter inclusion
- added --min_depth parameter (default 20)
- this is the minimum depth required for each nucleotide to not be masked to "N"
- updated to newest medaka version to support guppy 5.x models
- default medaka model is now
r941_min_sup_g507 - Please change accordingly via
--medaka_model(e.g. r941minhacg507 or r941minfastg507)
- default medaka model is now
This is a pre-release and it might contain some bugs
- Nextflow
Published by replikation over 4 years ago
porecov - vbz compression support
- vbz compression support added
- Nextflow
Published by replikation over 4 years ago
porecov - bug fix on nanopolish
- Fixed a small bug that failed the pipeline via nanopolish and the coverage plot
- thx @iferres
- Nextflow
Published by replikation over 4 years ago
porecov - alpha, delta etc.
- version push for pangolin and nextclade
- final report now includes the WHO names (via nextclade results)
- Nextflow
Published by replikation over 4 years ago
porecov - dry run and hotfix
- dry run implementation via stub for continuous integration of poreCov
- small bug fix on json output
- Nextflow
Published by replikation over 4 years ago
porecov - 0.9.0 New coverageplots and min read leangth support
- implemented CoVarPlot https://github.com/Psy-Fer/CoVarPlot (thx @hoelzer )
- removed the old coverage plot
- using the "primer trimmed bam file" from artic as "the bam output"
- implemented new guppy version and sup model
dna_r9.4.1_450bps_sup.cfg - implemented support for rapid barcoding kit via
--rapid - min and max read length can now be used for 1200 amplicon primers (see #116 )
- some bug fixes for multi-fasta inputs that could have occurred if they have the same name 3 times or more
- some adjustments in regards to the new pangolin versions
use the --update flag to always use the most recent pangolin lineage definition available
* this is independent of poreCov releases so you don't need to wait for a new poreCov release
- Nextflow
Published by replikation over 4 years ago
porecov - 0.8.3 bugfix
- fixed an issue that was preventing poreCov from doing guppy cpu based bascalling
- Nextflow
Published by replikation almost 5 years ago
porecov - bugfix on rki output csv table
- Fixed a rare occurrence where the RKI desh upload table could break
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.8.1 small bugfix
fixed an issue on --fastq_pass overwriting some reads when using a dir containing multiple e.g. "barcode01" dirs
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.8.0 New features and improvments
pangolin
- poreCov has now a
--updateflag which searches for the most recent pangolin version on dockerhub (#103)- this means you don't need to wait for a new poreCov release that updates pangolin
- (behind the scenes) we set up a cron job that tries to build a version-controlled pangolin every other day and pushes this to docker hub if it works without errors and contains all the data that poreCov needs
- as this feature might break the workflow it's deactivated by default to ensure stability
- pangolin version and pangoLEARN version are now shown on the final report for better reproducability
other inclusions and bugfixes
- supporting rapid barcode kits (RBK004) add
--rapidto the poreCov command - automatically start demultiplexing on
--fastq_passinput if no barcodes are detected #100 - bugfix: slurm profile was not a valid executed - now fixed, thx @KevinMenden #112
- slightly changed output-dir name, see #111
- included a new result dir
5.Genome-primer-repairwhich tells you which V3 or V1200 primers are needed to amplify only regions with ambiguous bases (to improve genome quality) - still a beta feature - feel free to report issues - improved CPU handling on guppy #ec77d43
- bugfix: removing reads that are too small was not working correctly (did not effected results, but still - its fixed now) #a9a81a1
- Added more error code for the user if e.g. not enough reads are available or no genomes were reconstructed
- this also points you to the read directory to check on e.g. how many barcodes you have or reads that are viral
- some visual updates on the final output report
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.12
- pangolin and nextclade version updates
- automatically removing whitespace from files used as input for
--samples - changed artics normalize to 500
- some more verbose exit statements during guppy basecalling to better understand what might be "missing" dependency wise
- set poreCovs parallel capabilities to "4" runs in parallel (default)
- should still work on "compute toasters"
- more verbose error statements for inputs (e.g. if you miss adding the fasta file to the
--fastaflag) - nanopolish skips basecalling if fastq data is provided, but this needs a sequence summary file in return (supplied via
--nanopolish)- error code added for this to explain the user what is missing
- bug fix if internet is unavailable for "get latest poreCov release" functions
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.11 update pangolin to v2.3.6
update pangolin to v2.3.6
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.9 Verbose Errors, outputs and more
- on startup the latest poreCov version available on Github is shown (#89)
- summary report file is also saved as tsv and excel file ( yes excel ;) thx @RaverJay ) (#88)
- nanopolish was added to poreCov, activate via
--nanopolishif--fast5is provided (#87) - pangolin version update
- error exit message if
--samplestable is not able to be merged with any of the barcodes to rename them (#86) - warning message if not enough barcode reads are available in ALL of the run (#86)
- this appears if no genome reconstruction is starting - I did not add a "exit" so that read classifications and qc will finish for trouble shooting
- reads files below 1.5 Mbyte are not removed if
--samplesis provided (should improve but not fix #92)- the sample name merge will remove "faulty barcodes"
- still wip, the issue is that e.g. for one end demultiplexing other barcodes are appearing that are not used (e.g. barcode 96 due to the read errors)
- the sample file needs to be used in the final report to add "missing" barcodes
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.8 update pangolin version
- update pangolin to v.2.3.5
- Nextflow
Published by hoelzer almost 5 years ago
porecov - 0.7.7 update pangolin version
- update to v2.3.4 pangolin
- Nextflow
Published by hoelzer almost 5 years ago
porecov - 0.7.6 singleton output of final FASTAs
- also output final and qc-ed FASTAs as singletons (one FASTA per sample)
- Nextflow
Published by hoelzer almost 5 years ago
porecov - 0.7.5 adjust pycoQC ram and cloud configs
adjust pycoQC ram and cloud configs
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.4 small fixes
- added some missing fixes from 0.7.3
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.3 bugfixes
- fixes "edge case" for integer only samples names breaking the report
- fixed rki output due to president updates
- added direct cleanup during kraken read classification (scratch was only moving files to a tmp directory and not removing them)
- TLDR: reduces the overall disk usage
- Nextflow
Published by replikation almost 5 years ago
porecov - 0.7.2 version updates, bugfixes, report improvements
- improved report in general
- improved read classification overview in the report
- update president and fixes on some minor issues
- Nextflow
Published by replikation about 5 years ago
porecov - 0.7.1 bugfixes, report improvements and clean ups
- Report % of Ns #66
- number of reads that are classified #62
- indel positions are reported #65
- reduced kraken footprint on server #59
- renamed
--dirto--fast52d2e2d740465e4128980547b8a848cd88f4e64f1 - renamed
--fastq_rawto--fastq_pass2d2e2d740465e4128980547b8a848cd88f4e64f1 --helpupdated and Readme updates
- Nextflow
Published by replikation about 5 years ago
porecov - 0.7.0 Major report update and various fixes extensions
- poreCov generates a nice and clean HTML report across your run
- multifasta support for the --fasta flag
- various tool version updates
- --rki produces "desh compatible" output (for upload to the desh portal)
- dag chart update to reflect what poreCov is doing
- [missing] readme cleanup
also thanks @RaverJay for the nice report file
- Nextflow
Published by replikation about 5 years ago
porecov - 0.6.1 fixes and updates
- bugfixes on kraken DB
- remove tree build
- update dag chart
- add alternative kraken db download on "error retry"
- update on Readme
- added nextclade mutations to json output (for mongo DB)
- improved cpu handling and help on local usage
- simplified work dir and database "dirs"
- pangolin version bump
- Nextflow
Published by replikation about 5 years ago
porecov - 0.6.0 read classification and nextclade
- kraken2 classification for reads + krona plot (to check for contamination and amount of stars reads)
- nextclade added, informs about clade mutations etc.
- Nextflow
Published by replikation about 5 years ago
porecov - 0.5.0 - lots of bug fixes and version updates
- --samples allows for sample renaming
- updates on president artic pangolin
- inclusion of most recent president to reflect quality statements
- Nextflow
Published by replikation about 5 years ago
porecov - 0.4.0 president for genome quality, and more
- code overhaul and bug fixing for upcoming additions
- next features will be clean user reports
- error strategy for cloud computing
- cloud computing compatible für google cloud life science
- workflow abstraction to allow for bigger workflow
- president (rki) inclusion
- Nextflow
Published by replikation about 5 years ago
porecov - update pangolin to v2.1.6
update pangolin to v2.1.6
- Nextflow
Published by replikation about 5 years ago
porecov - bugfix for no barcode run
bugfix for no barcode run (e.g. for flongle usage)
- Nextflow
Published by replikation about 5 years ago
porecov - update to newer pangolin version
update to newer pangolin version and some documentation fixes in --help and readme
- Nextflow
Published by replikation about 5 years ago
porecov - medaka vcf output fix
Small addition to the result dir: * added the VCF file of medaka to the output * closes #7
- Nextflow
Published by replikation over 5 years ago
porecov - Singularity fix
- fixed some singularity pathing issues
- added log10 scale to coverage plot
- Nextflow
Published by replikation over 5 years ago
porecov - 1200bp primer support and more
- added pycoQC as QC after guppy 76d9beb01cfddb35b202b4df37bfcfe3bd57d4c3
- added primer support for 1200 bp amplicons 76d9beb01cfddb35b202b4df37bfcfe3bd57d4c3
- added a non stringend demultiplexing option 276db9286cedf8f2ebda275f37d0e4e1813ac142
- various smaller bug fixes
- updated guppy c04646c5c03432ed768e127a5d13e620765082ff
- a few plot options and filtering for "N"s e18b2b631699c46455976247f6ef6652cfdd035f
- everything is described via
--help
- Nextflow
Published by replikation over 5 years ago