Releases: BU-ISCIII/buisciii-tools
Releases · BU-ISCIII/buisciii-tools
BUISCIII/buisciii-tools v2.2.12
Credits
Template fixes and updates
- Fixed IRMA's 99-stats lablog to take host reads from samtools stats instead of kraken #564.
- Fixed sgene_metrics.sh to handle warnings properly #565.
Modules
- Fixed finish module so that the clean module is run correctly #564.
- Fixed bioinfo_doc module so that a text file can properly be used for email notes #564.
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.11
Credits
Template fixes and updates
- Added micromamba environment PikaVirus_dev_2.6 to file hpc_slurm_pikavirus.config #535.
- Changed analysis_date in create_summary_report.sh to take properly dates from RSV services when using viralrecon #540.
- Fixed date formats for IRMA's template and excel_generator.py #549.
- Fixed the way whether samples are paired or single-end is detected #550.
- Removed pseudo_aligner parameter from RNASeq's lablog and added all missing symlinks in its RESULTS's lablog #552.
- Updated scratch.py and main.py to properly handle custom paths and temporary directories #555.
- Updated create_summary_report.sh to transform negative values into 0 #556.
- Updated the assembly stats script to handle files in RAW properly and when quast results are not available for any sample #557.
Modules
- Fixed clean module to handle subpaths stated in services.json #543.
- Fixed bioinfo_doc module to be able to indicate type (service_info or delivery) via CLI #558.
- Fixed the bioinfo_doc module to properly ask for email text notes and the scratch module to use proper scratch_tmp_path #559.
Added enhancements
- Added new script to download multiple SRA entries in fastq format when necessary #551.
Fixes
Changed
- Modified bu-isciii > buisciii for all commands in README text #548.
Removed
BUISCIII/buisciii-tools v2.2.10
Credits
Template fixes and updates
- Redefinition of analysis_date and lineage_analysis_date based on mapping folder and DOC config in viralrecon's template #523.
- Fix analysis_date and lineage_assignment_date format in create_summary_report.sh #525.
- Created a new script to correctly merge all nextclade results into one .csv file in IRMA's template, apart from updating lablog_irma_results with new symlinks to relevant files #526.
- Adapted create_summary_report.sh to handle multiple references and add lineage columns to pangolin .csv only if they do not exist yet #530.
Modules
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.9
Credits
Template fixes and updates
- Updated create_summary_report.sh to properly handle single end reads #509.
- Fix relative path handling in snpeff/snpsift annotation #509.
- Added sed to lablog_bam2fq so that _R1.bam is removed and the variable sample is created properly for those sample ids having several underscores (i.e. EPI_ISL_666)#490
- Update IRMA 99-stats lablog to raise Error if taxprofiler results are missing #515.
- Added a new lablog to create a .csv file for software versions in IRMA's template #514.
- Fixed wrong variable definition in IRMA's 99-stats lablog and added Nextclade's info into viralrecon's create_summary_report.sh script to be added into the mapping_illumina report #518.
- Added virus_sequence variable into IRMA's 99-stats lablog for the creation of the summary stats report #519.
Modules
Added enhancements
Fixes
Changed
Removed
BUISCIII/buisciii-tools v2.2.8
Credits
Template fixes and updates
- Updated snippy template, now using a modified version of snippy with different low coverage masking#489
- Update PlasmidID Report Generation to Output Summary by Sample #483
- Update of the execution of summary_report_pid.py in plasmidID lablog #484
- Added
sort -uto wgs_metrics_all.txt file generation command in 99-stats lablog (snippy template) #494 - Avoided error messages when running 99-stats lablog several times (snippy template) #495
- Added Nextclade, variant calling and stats extraction scripts into the IRMA template #499.
- Added flu_type to summary_stats (IRMA template) #501.
- Fixed errors in IRMA template and fixed errors in irma2vcf script #500
- Modified artic bed version in lablog_viralrecon for SARS-CoV-2 analysis #505
Modules
Added enhancements
- Implemented multi-attachment support in Bioinfo-doc email sending workflow #488
- Added kmerfinder to snippy template #498
Fixes
Changed
- Expanded the maximum width of email body to 1000px for better desktop display #488
- Corrected the logo URL to use a direct raw link for proper rendering in email clients #488
Removed
BUISCIII/buisciii-tools v2.2.7
Credits
Template fixes and updates
- Fixed bug in 08_create_quality_control_summary.sh (viralrecon template) #447.
- Updated
services.jsonfile in order to properly delete folders and files when running clean module #451. - Add assets for Updating Lineage-Defining Mutations from outbreak-info #452
- Fix get_percentage_LDM.py to Use Versioned CSV File#453.
- Moved
lablog_bam2fq.shtoRAW/** to centralize BAM-to-FASTQ processing #455 - Updated
_01_bam2fq.shto correctly detect all BAM files inRAW/#455 - Refactored
_02_pgzip.shto compress.fastqfiles and remove uncompressed versions #455 - Created
_03_symlink.shto manage symbolic links inANALYSIS/00-reads/, preventing broken links #455 - Removed single quotes from sftp_copy in configuration.json #458
- Fixed and enhanced some issues for lablog_viralrecon #461
- Update sftp_users.json with new user for e.abascal #464
- Update sample handling in get_percentage_LDM #465
- Added _02_filter_results.sh script to pikavirus template #466
- Changed short_obx for middle_idx in 02-clean.sh #468
- Update exometrio lablog to Handle Fourth Individual #469
- Update get_percentage_LDM.py to read sample column as string #470
- Updated ivar varsion in viralrecon template to makwe it work with IonTorrent data #471
- Update get_percentage_LDM.py to Handle Cases with No Lineage Found in outbreak.info CSV #473
- Added autorun.sh script for automation of multiple sbatch running in viralrecon pipeline #474
- Modified clean.py in order to properly delete exact matching-name folders and files #476
- Added information on the period of permanence of the results in the sftp folder in email template #477
Modules
Added enhancements
Fixes
Changed
Removed
Requirements
BUISCIII/buisciii-tools v2.2.6
Credits
Template fixes and updates
- User added to sftp_user.json #404.
- Fix archived path #405
- Updated characterization/03-amrfinderplus lablog with summary generator #406
- Updated lablog_viralrecon to replace conda by micromamba, and updated the output message from remove_columns_mapping_table.sh #409
- Created lablog_bam2fq in viralrecon's template #409
- Replaced bu_isciii by buisciii where necessary, and bu_isciii by buisciii-tools in init.py #411
- Added versions for all dependencies in requirements.txt #411
- Implemented a non-interactive mode for running lablog_viralrecon #410
- Fixes in several service templates #414
- Modified path for temporal files in irma_config.sh #414
- Modified field (cut) where extracted flu type information in lablog_irma_results #414
- Implemented QC scripts into viralrecon template #422
- Fixed minor mistakes in chewBBACA's template #425.
- Fixed some issues in outbreak services #428
- Add micromamba activation comment to viralrecon template lablog and add total_N_count to sgene_metrics script#432
- Added last_folder field to plasmidid_assembly service in services.json #434
- Fixed bioinfo-doc crashing after resuming #435
- Fixed create_summary_report.sh to latest /data/ucct/bi/ layout #436
- Changed taxprofiler lablog to skip kaiju, centrifuge and metaphlan #439
Modules
Added enhancements
Fixes
- Fixed drylab_api.py to show a more descriptive message when the resolution ID does not exist #437.
Changed
Removed
BUISCIII/buisciii-tools v2.2.5
Credits
Template fixes and updates
- Changed mag.md by taxprofiler.md in assets/reports #396.
- Modified irma_output.md to include only taxprofiler #396.
- Updated services.json with taxprofiler #396.
- Created a lablog file for chewbbaca/REFERENCES #396.
- Updated lablog_irma and renamed ANALYSIS01 folders #396.
- Updated IRMA template and its files to include RSV #396.
- Updated chewbbaca results' lablog to include cgMLST_MSA.fasta #396.
- Updated exometrio and wgstrio results lablogs not to include exomiser's html #396.
- Created plasmidid's results lablog #396.
- Updated mtbseq's lablog to remove unnecessary single quotes #396.
- Fixed snippy's lablog to be better explained and updated its results' lablog #396.
- Updated version in pyproject.toml and main.py #396.
Modules
Added enhancements
Fixes
Changed
- Replaced setup.py by pyproject.toml #396.
Removed
- Removed MAG template and replaced it with taxprofiler #396.
BUISCIII/buisciii-tools v2.2.4
BUISCIII/buisciii-tools v2.2.3
Credits
Code contributions to the new version:
Template fixes and updates
- Updated sftp_user.json, added the locus-tag option for the PROKKA process in the bacass config file and changed new_service.py so that integrity is checked only for the samples of interest #363.
- Replaced /data/bi/ by /data/ucct/bi/ #380.
- Updated bacass version in all pertinent files #380.
- Updated read length variable definition when creating the mapping_illumina.tab file #380.
- Updated create_irma_stats.sh to include %mapped_reads #380.
- Changed "Buenas" by "Estimado/a" in email.j2 #380.