3.5.3

This patch release fixes an issue (#22) with Illumina paired-end read analysis by IRMA producing empty consensus sequences when the forward and reverse reads do not contain "1:N:0:." or "2:N:0:." in the FASTQ header lines.

What's Changed

• Fix issue with Illumina PE read headers for IRMA analysis by @peterk87 in #90
• Release 3.5.3 by @peterk87 in #91

Full Changelog: 3.5.2...3.5.3

3.5.2

This patch release fixes a few issues when running the pipeline.

Changes

• fix: better handling of empty IRMA consensus sequences to avoid downstream analysis errors with VADR and BLASTN (peterk87/nf-flu #22)
• fix: Clair3 versions.yml indentation issue (#87)
• fix: removed capturing of cat and gzip versions in CAT_ILLUMINA_FASTQ process (#46) to avoid issue in some execution environments.
• docs: update README.md

What's Changed

• Fix multiple issues by @peterk87 in #88
• Release 3.5.2 by @peterk87 in #89

Full Changelog: 3.5.1...3.5.2

3.5.1

This patch release fixes an issue (#84) with long sample names (over 50 characters) causing VADR to fail. --noseqnamemax has been added to the default arguments for VADR to avoid this issue.

Changes

• fix: Added --noseqnamemax to VADR default arguments to avoid issues with long sample names causing VADR to fail.
• config: Output directory paths for IRMA and Bcftools consensus VADR annotation results were made more explicit and clear for the Illumina workflow.

What's Changed

• Fix issue 84; no VADR seq name max length by @peterk87 in #85
• Release 3.5.1 by @peterk87 in #86

Full Changelog: 3.5.0...3.5.1

3.5.0

This release expands the Illumina workflow by adding BLAST analysis, coverage plots, variant calling, and MultiQC reports. Modifications were made to existing modules, and new modules were added.

Changes

• feat: Added variant calling, BLAST analysis, coverage plots, and MultiQC to the Illumina workflow to match the capabilities of the Nanopore workflow.
• feat: Introduced a new module, Freebayes, for Illumina variant calling.
• refactor: Rearranged the Illumina workflow to integrate the new changes and enhance compatibility.
• update: Updated Bcftools filtering to add missing tags with fill-tags plugin and to set genotype with the setGT plugin based on major/minor_allele_fraction thresholds to influence consensus sequence output.
• config: Changed process labels for IRMA and MultiQC modules to "long" to avoid timeouts for large short-read datasets.
• enhance: Changed VADR staged file to use the FTP NCBI link to bypass certificate issues during Nextflow staging.
• rollback: Reverted VADR containers to an earlier version to resolve potential issues on Singularity.
• refactor: Rearranged modules_illumina.config for consistency with the updated workflow.
• container: Switched to Biocontainers images for Clair3 v1.0.10. Issue with full alignment not working with the Biocontainers Docker/Apptainer images seems to have been resolved. This should also resolve an issue with CI where it would fail due to not being able to pull the official Clair3 image hbukal/clair3 from Docker Hub.
• dev: Added tests/run-illumina-test.sh to make it more convenient to run the Illumina test locally with the same conditions as GitHub Actions CI.

What's Changed

• Switch to Clair3 Biocontainers image, add Illumina test script by @peterk87 in #82
• Illumina expansion by @ameknas-phac in #78
• Release 3.5.0 by @peterk87 in #83

New Contributors

• @ameknas-phac made their first contribution in #78

Full Changelog: 3.4.1...3.5.0

3.4.1 - Illumina FASTQ concatenation fix

This patch release fixes an issue (#75) with CAT_ILLUMINA_FASTQ where 1:N:0:. or 2:N:0:. may be mistakenly appended
to Q-score lines beginning with @.

Changes

• fix: updated Perl regex to better match Illumina FASTQ header lines starting with @. At least one space is expected in the header line. Match regex has been changed to /^@.* .*/ from /^@.*/ so hopefully Q-score lines should not be matched anymore.
• dev: replaced nf-core/modules DUMPSOFTWAREVERSIONS with mqc_versions_table v0.2.0 Nim statically compiled binary to parse versions.yml and output necessary YAML with HTML content for display of process and tool versions table in MultiQC report. In theory DUMPSOFTWAREVERSIONS should be using the same Docker/Singularity image/Conda env as the MultiQC process, but DUMPSOFTWAREVERSIONS uses an older version of MultiQC and only uses it for the pyyaml library. mqc_versions_table was developed to handle this instead with a small 200KB binary instead.
• dev: harmonize Docker/Singularity containers and Conda envs used across processes.
• ci: use symlink mode for publishDir by default for test_nanopore.config and test_illumina.config to limit disk usage during CI.
• Updated to Bioconda channel VADR v1.6.4 since the STAPH-B offered container with the flu model packaged is very large at 6GB vs 1.45GB for quay.io/biocontainers/vadr 1.6.4. However, it's now required that the flu model be downloaded and installed prior to VADR annotation with --vadr_model_targz. The default model tarball is the vadr-models-flu-1.6.3-2.tar.gz (38MB) from the NCBI FTP site uploaded to Zenodo.

What's Changed

• Fix cat_illumina_fastq header match Perl regex by @peterk87 in #76
• Release 3.4.1 by @peterk87 in #77

Full Changelog: 3.4.0...3.4.1

3.4.0 - VADR Annotation

This release adds Influenza virus sequence annotation using VADR.

Changes

• Add VADR for Influenza consensus sequence annotation
• Add table2asn for Feature Table conversion to Genbank
• Add pre- and post-table2asn processing to workaround sequence ID length limits imposed by table2asn when converting from Feature Table format to Genbank

What's Changed

• Add VADR Influenza sequence annotation by @peterk87 in #73
• Release 3.4.0 by @peterk87 in #74

Full Changelog: 3.3.10...3.4.0

3.3.10 - MultiQC report fix

Fix MultiQC report generation due to module filter paths not working like in v1.12.

Software Updates

• multiqc: 1.21 -> 1.22.1

Changes

• test: add tests/run-nanopore-test.sh to conveniently run Nanopore test locally

What's Changed

• Fix MultiQC report generation by @peterk87 in #71
• Release 3.3.10 by @peterk87 in #72

Full Changelog: 3.3.9...3.3.10

3.3.9 - software updates

What's Changed

• Update software to latest versions by @peterk87 in #69
• Release 3.3.9 by @peterk87 in #70

Full Changelog: 3.3.8...3.3.9

3.3.8 - ambiguous bases in consensus fix

This bugfix patch release fixes an issue where a large number of ambiguous bases in the IRMA consensus can hinder
reference selection (#67). This release also addresses an issue with using the Clair3 Biocontainers image resulting in
incomplete variant calling results, affecting nf-flu executions with the docker or singularity profiles. The
official Clair3 image is used instead. nf-flu executions using Conda and Mamba are unaffected.

Changes

• Create majority consensus from IRMA allAlleles.txt files for BLASTN search
• Add irma-alleles2fasta.v, statically compiled binary (irma-alleles2fasta) and Bash build script for parsing IRMA
  allAlleles.txt to output naive majority consensus (i.e. This bugfix patch release fixes an issue where a large number of ambiguous bases in the IRMA consensus can hinder
  reference selection (#67). This release also addresses an issue with using the Clair3 Biocontainers image resulting in
  incomplete variant calling results, affecting nf-flu executions with the docker or singularity profiles. The
  official Clair3 image is used instead. nf-flu executions using Conda and Mamba are unaffected.

Changes

• Create majority consensus from IRMA allAlleles.txt files for BLASTN search
• Add irma-alleles2fasta.v, statically compiled binary (irma-alleles2fasta) and Bash build script for parsing IRMA
  allAlleles.txt to output naive majority consensus (i.e. whatever the top non-dash allele is at each position) so
  that the sequence used for BLASTN search does not contain any ambiguous bases.
• Updated nanopore.nf subworkflow to use IRMA majority consensus with no ambiguous bases for BLASTN search so that
  longer more contiguous matches are possible to aid in top reference sequence selection in some cases.
• Updated parse_influenza_blast_results.py to better handle extraction of sample name and segment number from BLASTN
  query accession/version (qaccver).
• Using official Clair3 Docker image and updating Clair3 to v1.0.5whatever the top non-dash allele is at each position) so
  that the sequence used for BLASTN search does not contain any ambiguous bases.
• Updated nanopore.nf subworkflow to use IRMA majority consensus with no ambiguous bases for BLASTN search so that
  longer more contiguous matches are possible to aid in top reference sequence selection in some cases.
• Updated parse_influenza_blast_results.py to better handle extraction of sample name and segment number from BLASTN
  query accession/version (qaccver).
• Using official Clair3 Docker image and updating Clair3 to v1.0.5

What's Changed

• Fix #67 where IRMA consensus ambiguous bases can result in poor reference sequence selection by @peterk87 in #68

Full Changelog: 3.3.7...3.3.8

3.3.7 - IBV PB1/PB2 mislabeling bugfix patch release

This bugfix patch release fixes an issue with mislabeling of PB1 and PB2 segments for Influenza B virus results (#65).

What's Changed

• Fix PB1 and PB2 mislabeling in IBV by @peterk87 in #66

Full Changelog: 3.3.6...3.3.7