Credits
Code contributions to the new version:
- [Pablo Mata](https://github.com/Shettland)
- [Jaime Ozáez](https://github.com/jaimeozaez)
- [Sara Monzón](https://github.com/saramonzon)
- [Sarai Varona](https://github.com/svarona)
- [Daniel Valle](https://github.com/Daniel-VM)
- [Víctor López](https://github.com/victor5lm)
- [Juan Ledesma](https://github.com/juanledesma78)
Template fixes and updates
- Updated documentation and results markdown for viralrecon, pikavirus and MAG [247](https://github.com/BU-ISCIII/buisciii-tools/pull/247)
- Added documentation and results markdown for RNAseq [248](https://github.com/BU-ISCIII/buisciii-tools/pull/248)
- Added documentation both output and results for plasmidID[258](https://github.com/BU-ISCIII/buisciii-tools/pull/258)
- Added markdown of assembly analysis procedure [244](https://github.com/BU-ISCIII/buisciii-tools/pull/244)
- Added output and results markdowns for ExomeEB, ExomeTrio and WGStrio [249](https://github.com/BU-ISCIII/buisciii-tools/pull/249)
- Added markdown of assembly results folder [250](https://github.com/BU-ISCIII/buisciii-tools/pull/250)
- Updated lablog results filenames where necessary (IRMA, seekndestroy, viralrecon and genomeev) [253](https://github.com/BU-ISCIII/buisciii-tools/pull/253)
- Added output and results markdowns for cgMLST/wgMLST [255](https://github.com/BU-ISCIII/buisciii-tools/pull/255)
- Added markdown for IRMA [256](https://github.com/BU-ISCIII/buisciii-tools/pull/256)
- Included RESULTS/lablog for exomeeb, exometrio and wgstrio templates and updated files to clean [260](https://github.com/BU-ISCIII/buisciii-tools/pull/260)
- Changed scratch copy queue to middle_obx
- Included missing folders in wgstrio template
- Changed exomiser-html-description to png format and fixed location of irma-sarek markdowns [261](https://github.com/BU-ISCIII/buisciii-tools/pull/261)
- Updated configuration.json so that either idx or obx is used in case one of these queues is full [263](https://github.com/BU-ISCIII/buisciii-tools/pull/263)
- Updated lablog_viralrecon script for the automation of the setup of viralrecon services. [264](https://github.com/BU-ISCIII/buisciii-tools/pull/264)
- Included MULTIQC v.1.19 in viralrecon.config to fix error with string and numeric samples [267](https://github.com/BU-ISCIII/buisciii-tools/pull/267)
- Updated MTBSeq template to fit bacass pipeline. [268](https://github.com/BU-ISCIII/buisciii-tools/pull/268)
- IRMA template modified in order to avoid average overload.
- Added "01" to results folder creation in assembly template.
- Some prompt answers limited to 1 character in lablog_viralrecon.
- Created lablog_mtbseq_results. [270](https://github.com/BU-ISCIII/buisciii-tools/pull/270)
- PR 271. Closes [235](https://github.com/BU-ISCIII/buisciii-tools/issues/235), [#228](https://github.com/BU-ISCIII/buisciii-tools/issues/228) and [#196](https://github.com/BU-ISCIII/buisciii-tools/issues/196)
- Included annotated tab description in exome-trios markdowns [273](https://github.com/BU-ISCIII/buisciii-tools/pull/273)
- Installed all necessary singularity images and modified all templates so that, instead of using conda environments or loaded modules, the corresponding singularity images are used [272](https://github.com/BU-ISCIII/buisciii-tools/pull/272)
- Updated sarek version in exomeeb, exometrio and wgstrio templates [277](https://github.com/BU-ISCIII/buisciii-tools/pull/277)
- Extension file of all_samples_virus_table_filtered (from csv to tsv) in lablog_viralrecon_results changed [278](https://github.com/BU-ISCIII/buisciii-tools/pull/278)
- Fixed singularity-images path when updating pangolin database in lablog_viralrecon. Added line break after prompted input. [282](https://github.com/BU-ISCIII/buisciii-tools/pull/282)
- Updated characterization and snippy templates to fit bacass pipeline. Corrected path in 05-iqtree in snippy template. [283](https://github.com/BU-ISCIII/buisciii-tools/pull/283)
- Included multiqc_report.html in RESULTS folder in every service, where necessary [265] (https://github.com/BU-ISCIII/buisciii-tools/pull/265)
- Added MAG tempalte and removed MAG from other templates [288](https://github.com/BU-ISCIII/buisciii-tools/pull/288)
- Added amrfinderplus to characterization template. [289] (https://github.com/BU-ISCIII/buisciii-tools/pull/289)
- Updated all files so that paths referring to /pipelines/ are updated according to the new structure [287](https://github.com/BU-ISCIII/buisciii-tools/pull/287)
- Updated assembly, ariba, snippy, amrfinderplus and iqtree templates, removed genomeev and mtbseq_assembly templates and updated services.json [295](https://github.com/BU-ISCIII/buisciii-tools/pull/295)
- Changed viralrecon's lablog so that references are available within refgenie [296](https://github.com/BU-ISCIII/buisciii-tools/pull/296)
- Updated services.json, mtbseq's lablog, viralrecon's lablog and assembly's config file [299](https://github.com/BU-ISCIII/buisciii-tools/pull/299)
- Added lablog to automate gene characterization with emmtyper, including unzipping assemblies. [300](https://github.com/BU-ISCIII/buisciii-tools/pull/300)
- Fixed 99-stats (MAG) template. [301](https://github.com/BU-ISCIII/buisciii-tools/pull/301)
- Created a python script to process IRMA's results and create a standard vcf file against reference. [304](https://github.com/BU-ISCIII/buisciii-tools/pull/304)
- Fixed IRMA's lablog so that the sequences of the samples are not displayed several times neither in the .txt files of each influenza type nor in all_samples_completo.txt [305](https://github.com/BU-ISCIII/buisciii-tools/pull/305)
- Modified bioinfo_doc.py so that new lines in the delivery message are applied in the email [307](https://github.com/BU-ISCIII/buisciii-tools/pull/307)
- Added several improvements in lablog_viralrecon (created log files, modified check_references function behaviour, enabled config files regeneration) [306](https://github.com/BU-ISCIII/buisciii-tools/pull/306)
- Fixed bug when lablog_viralrecon tries to download references that don't belong to any family. [310](https://github.com/BU-ISCIII/buisciii-tools/pull/310)
- Added mvmoneo to SFTP users. [317](https://github.com/BU-ISCIII/buisciii-tools/pull/317)
- Added scripts for time series RNAseq and updated differential expression code for differentially expressed transcripts [316](https://github.com/BU-ISCIII/buisciii-tools/pull/316).
- Added bbaladron to SFTP users [316](https://github.com/BU-ISCIII/buisciii-tools/pull/316).
- Added new template for comprehensive taxonomy profiling using the nf-core/taxprofiler pipeline [320](https://github.com/BU-ISCIII/buisciii-tools/pull/320).
- Added full execution support for the MAG template [321](https://github.com/BU-ISCIII/buisciii-tools/pull/321).
- Added labels to services.json and updated bioinfo_doc.py and jinja_template_delivery.j2 so that software versions data is displayed in the delivery pdf [330](https://github.com/BU-ISCIII/buisciii-tools/pull/330).
- Updated several templates (singularity images, outdated paths, improvements, etc) [331](https://github.com/BU-ISCIII/buisciii-tools/pull/331)
- Added permissions fixing after running scratch_copy, as well as a new fix-permissions module in the tools [332](https://github.com/BU-ISCIII/buisciii-tools/pull/332).
- Updated MAG lablogs and utils.py [334](https://github.com/BU-ISCIII/buisciii-tools/pull/334).
- Updated some files (setup.py, __main__.py, README, etc) for the 2.2.0 release [335](https://github.com/BU-ISCIII/buisciii-tools/pull/335).
Modules
Added enhancements
- PR [274](https://github.com/BU-ISCIII/buisciii-tools/pull/274): added `--dev` option, configuration dev and test folder structure.
- PR [276](https://github.com/BU-ISCIII/buisciii-tools/pull/276): wkhtmlpdf does not need absolute path to executable. Added better error handling when executable does not exists.
- PR [288](https://github.com/BU-ISCIII/buisciii-tools/pull/288) Allowed to handle more than one service at a time, related to issue [#217](https://github.com/BU-ISCIII/buisciii-tools/issues/217)
Fixes
- Fixed archive module. Updated correct header for scout tsv [258](https://github.com/BU-ISCIII/buisciii-tools/pull/258).
- Fixed clean module. Corrected purge_files function. Renaming stage moved from clean to rename_nocopy option. Updated services.json file with correct paths for some services. [280](https://github.com/BU-ISCIII/buisciii-tools/pull/280)
- Fixed autoclean-sftp function. [281](https://github.com/BU-ISCIII/buisciii-tools/pull/281)
- Fixed bioinfo_doc.py. Modified it so that this module creates a .pdf file including new-line characters, without merging lines into one single line [259](https://github.com/BU-ISCIII/buisciii-tools/pull/259).
- PR [288](https://github.com/BU-ISCIII/buisciii-tools/pull/288) Fixed updating service's state to in_progress multiple times, related with issue [#285](https://github.com/BU-ISCIII/buisciii-tools/issues/285)
- Review and update of services.json for files and folders cleaning [318](https://github.com/BU-ISCIII/buisciii-tools/pull/318).
Changed
- Forcing python lint to success if no .py files are in PR [279](https://github.com/BU-ISCIII/buisciii-tools/pull/279)
Removed
Requirements