measeq - 0.4.0

Release adding in more data tracking, specifically for the N450 region along with fixes/adjustments to the DSId calling system (always ran now vs just run when providing info)

Added

• 3 columns to final Excel and CSV file PR #12
  • N450_completeness
  • N450meandepth
  • N450_status
• Fail tracking for all samples and runs where every sample fails PR #12

Adjusted

• Adjusted the DSId final report page to have a list of all individual sample calls and the summary data shown
• Added the N450 status to the initial report summary page
• Always run the DSId check even with no database fasta file
  • Everything will be labeled as novel-hash but it will group them up
• Updated CI tests

- Nextflow
Published by DarianHole 10 months ago

measeq - 0.3.2

Release focusing on cleaning up some of the DSId reporting along with fixing a few small bugs

Added

• DSId tab to final HTML report for DSId summary information if a DSId file was given as input PR #10
• New overall.xlsx final QC file based on adding in a few more columns PR #10
  • genome_fasta and N450_fasta that contain fasta formatted sequence data
  • This broke the CSV file version parsing so that remains unchanged to get metadata to IRIDANext

Adjusted

• Fixed a bug with MeaSeq Report summary table not correctly linking to certain samples PR #10
• Removed versions.yml from being created during final report as versions already were reported PR #10
• Adjusted code for final report row formatting to match throughout Rmd files PR #10
• DSId assignment changes PR #10
  • Hash adjusted to 7 characters
  • Semi-Complete removed to just be Incomplete
• New container for the MAKEFINALQC_CSV step to remove artic container PR #10
  • Adds in openpyxl

- Nextflow
Published by DarianHole 11 months ago

measeq - 0.3.1

Adjusted

• Fixed a bug where the irida json file wasn't being populated with metadata PR #7
• Adjusted Illumina nf-test to use the sample_name field of the samplesheet to test that it works PR #7

Removed

• Normalized median read depth plot for now as it overlaps the full depth one too much PR #7

- Nextflow
Published by DarianHole 11 months ago

measeq - 0.3.0

Added

• CI tests and Linting PR #6
• Providence to final Measeq_Report.html file PR #5
• Approximate genome position annotation to final report figures PR #5
• nf-validation to work with IRIDA Next PR #6
• nf-iridanext to work with IRIDA Next PR #6
• nf-prov to allow some more providence options PR #5
• Hashes to novel DSId calls so that in the same run new DSIds will match PR #5
  • And they will match in other locations as well
• min_indel_threshold parameter to set the minimum indel threshold required to call an indel PR #6

Adjusted

• Output directories for Nanopore process in the modules.config file PR #6
• Updated artic version from 1.6.2 --> 1.7.4 for nanopore pipeline PR #6
• Ambiguous position handling for illumina data PR #5
  • Specifically for rare postions where there was a low-supported INDEL along with a SNP
• Negative control default string to add in 'en' PR #5
• Samtools depth meta1 to meta as it was breaking the IRIDA-Next plugin PR #6
• Minimum nextflow version required to 24.10.0 PR #5
• Samplesheet input added a sample_name column to work with IRIDA Next PR #6

Removed

• nf-schema and associated workflows PR #6

- Nextflow
Published by DarianHole 11 months ago

measeq - 0.2.1-dev

v0.2.1 - [2025-06-12]

Added

• New plots to the summary table for the final report
  • Summary sequencing depth plots
  • No longer stand-alone as it can get a bit large, a smaller report will be made later
• Allow primer schemes to have different direction extensions in the names
  • _L, _R, _FORWARD, _REVERSE, _F
  • Added in proper errors for if the primer file was not formatted correctly
• Readme updates for primers

Bugfixes

• genome_completeness fixed to genome_completeness_percent in the negative control checking

Removed

• N plots of the final report to help lower size and speed up opening

- Nextflow
Published by DarianHole about 1 year ago

measeq - 0.2.0-dev

v0.2.0-dev - [2025-06-06]

Dev release of all of the nextflow code and updates to the pipeline. All of the Illumina processing should be working well! The nanopore processing side still needs a bit more to match the illumina which is why it is a dev release

Added

• All of the pipeline has been rewritten in Nextflow
• Illumina paired-end sequencing workflow added
  • Freebayes for variant calling over ivar variants/consensus previously
• Nanopore (initial) workflow added
  • clair3
• DSId assignment added when using --dsid fasta parameter
  • Based on full sequence match
• Summary outputs added
  • Amplicon summary report
  • The current Rmarkdown report needs to be fixed for the new outputs

- Nextflow
Published by DarianHole about 1 year ago