rnavar - nf-core/rnavar 1.2.0 - Black Bebop

What's Changed

• Add seq2hla for ClassI/II hlatyping by @FriederikeHanssen in https://github.com/nf-core/rnavar/pull/225
• update vep to 114.2 - enable bcftools annotation for real by @maxulysse in https://github.com/nf-core/rnavar/pull/224
• Prepare release 1.2.0 by @maxulysse in https://github.com/nf-core/rnavar/pull/227
• Address comments from release review by @maxulysse in https://github.com/nf-core/rnavar/pull/229
• Release 1.2.0 by @maxulysse in https://github.com/nf-core/rnavar/pull/230

Full Changelog: https://github.com/nf-core/rnavar/compare/1.1.1...1.2.0

- Nextflow
Published by maxulysse 6 months ago

rnavar - nf-core/rnavar 1.1.1 - Brave Benatar

What's Changed

• bump back to dev by @nvnieuwk in https://github.com/nf-core/rnavar/pull/203
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in https://github.com/nf-core/rnavar/pull/209
• Fix pair ended fastq merging by @maxulysse in https://github.com/nf-core/rnavar/pull/211
• update reports by @maxulysse in https://github.com/nf-core/rnavar/pull/212
• update all modules by @maxulysse in https://github.com/nf-core/rnavar/pull/213
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in https://github.com/nf-core/rnavar/pull/215
• moving params out of workflows and multiQC to the root main.nf by @maxulysse in https://github.com/nf-core/rnavar/pull/216
• Update nextflow_schema.json: remove fasta from required by @FriederikeHanssen in https://github.com/nf-core/rnavar/pull/218
• nf-core pipelines bump-version 1.1.1 by @maxulysse in https://github.com/nf-core/rnavar/pull/221
• fix conda tests by @maxulysse in https://github.com/nf-core/rnavar/pull/222
• Release 1.1.1 by @maxulysse in https://github.com/nf-core/rnavar/pull/220

New Contributors

• @FriederikeHanssen made their first contribution in https://github.com/nf-core/rnavar/pull/218

Full Changelog: https://github.com/nf-core/rnavar/compare/1.1.0...1.1.1

- Nextflow
Published by maxulysse 7 months ago

rnavar - nf-core/rnavar 1.1.0 - Mighty Milano

1.1.0 - 2025-04-10

Added

• #116 - Added unzip from nf-core modules for working with unzipped fasta and gtf files
• #157 - Added support for bam and cram input files
• #169 - Added the --star_max_intron_size parameter to set the --alignIntronMax argument in STAR
• #180 - Added support for UMI extraction. Specify --extract_umi to enable this feature
• #187 - Added unit tests for local subworkflows and processes
• #193 - Added support for vcf.gz input files

Changed

• #78 - Add a gvcf file generated by sample
• #78 - Merge on exome.bed
• #78 - Add option to choose the type exon/transcript/gene of studied feature in GTF
• #95 - Template update for nf-core/tools v2.9
• #97 - Template update for nf-core/tools v2.10
• #109 - Update all modules
• #111 - Template update for nf-core/tools v2.11
• #117 - Template update for nf-core/tools v2.11.1
• #120 - Template update for nf-core/tools v2.12
• #140 - Template update for nf-core/tools v2.14.1
• #153 - Template update for nf-core/tools v3.0.2
• #153 - Converted pytest tests to nf-test tests
• #161 - Template update for nf-core/tools v3.2.0
• #167 - Removed the strandedness field from the samplesheet as it wasn't used in the pipeline.
• #172 - Added support for TSV, JSON and YAML samplesheets
• #178 - Implement automatic sharding for nf-test tests
• #182 - Bumped all modules to the latest version (as of 03/03/2025)
• #185 - Updated the documentation
• #193 - Replaced param annotate_tools with tools
• #193 - Parameter snpeff_genome value is now contained in the snpeff_db parameter

Fixed

• #97 - Update all gatk4 modules to disable JVM hotspot
• #98 - Restore annotation
• #102 - Fix process name SNPEFF_SNPEFF
• #105 - Fixing ch_dict
• #106 - Fixing vep_cache
• #107 - Fixing star index + single read files
• #124 - Fixed s3 bucket path in conditional statement for SnpEff cache
• #127 - Fixed s3 bucket path in conditional statement for VEP cache
• #130 - Added missing "def" in local variables
• #132 - Added missing variantcaller key to meta map, to fix null value in publishDir
• #136 - Replaced unzip module with gunzip, removed unzip module
• #138 - Proper usage of GVCF
• #142 - Fix dbsnp channels
• #143 - Use DROP_MISSING_CONTIGS by default in GATK4_BEDTOINTERVALLIST
• #144 - Change gatk_vf params from integer to floats
• #145 - Converted star_index and gtf emit channels from queue to value channels in PREPARE_GENOME subworkflow
• #149 - Updated chgtf and chfasta_fai channels emitted by main.nf
• #158 - Fixed language server errors and warnings
• #159 - Fixed a couple of bottlenecks in the pipeline
• #168 - Allow integer values for --vep_cache_version and --snpeff_db.
• #170 - Fixed pipeline failure when running --skip_intervallisttools.
• #171 - Fixed the --dbnsp and --known_indels handling. Uncompressed files are now allowed as inputs to the pipeline as the pipeline will automatically compress these.
• #172 - Fixed the parameters JSON schema so the pipeline does better input validation.
• #173 - Added STAR index version control, the pipeline will now automatically detect a wrong STAR index version an create the correct index instead.
• #175 - Fixed the handling of GFF files so they are now correctly being used.
• #177 - Added a check and filter step for unknown regions in the exon BED. You can disable this check with --skip_exon_bed_check.
• #184 - Added an early error when --dbsnp and/or --known_indels were missing and base recalibration wasn't turned off.
• #194 - Only create the STAR index when FASTQ files are used in the input.

Dependencies

| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | bcftools | 1.17 | 1.20 | | bedtools | 2.31.0 | 2.31.1 | | fastqc | 0.11.9 | 0.12.1 | | gatk | 4.2.6.1 | 4.6.1.0 | | mosdepth | 0.3.3 | 0.3.10 | | multiqc | 1.15 | 1.18 | | picard | 3.1.0 | 3.3.0 | | samtools | 1.17 | 1.21 | | star | 2.7.10a | 2.7.11b | | vep | 111.0 | 113.4 | | r-base | 3.5.0 | 3.5.1 |

Parameter

| Old name | New name | | ---------------- | -------- | | annotate_tools | tools | | snpeff_genome | |

- Nextflow
Published by nvnieuwk 11 months ago

rnavar - nf-core/rnavar v1.0.0 - Tiny Firefly

[1.0.0] - 2022-06-20

First production release of the pipeline with the latest software versions.

This version is based on GATK4 best-practices for RNAseq [Ref] and it includes:

Added

• FastQC v0.11.9 for read-level QC and summary.
• STAR v2.7.9a for read alignment to reference genome.
• Samtools v1.15.1 for alignment sorting, indexing, and statistics.
• GATK v4.2.6.1 for alignment post-processing, variant calling, and filtration.
• Tabix v1.11 for indexing VCF files.
• SnpEff v5.0 for variant annotation.
• Ensembl VEP v104.3 for variant annotation.
• MultiQC v1.12 for QC summary report.
• Scatter method i.e., split one gene interval list into many interval files to run multiple processes in parallel to speed up analysis.

Thanks to everyone that contributed to this release. Special thanks to @maxulysse, @FriederikeHanssen, and @chris-cheshire for your reviews and valuable suggestions.

- Nextflow
Published by praveenraj2018 over 3 years ago