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 ch_gtf and ch_fasta_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

Parameter