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nf-core/seqinspector: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

dev

Added

  • #109 Adds ToulligQC module for long read QC
  • #134 Added sequali module.
  • #202 Added support for fasta fai file as input (via params or igenomes) for the pipeline
  • #204 Added Fastp module
  • #206 Added FASTQE for more comprehensive QC of FASTQ files
  • #208 Add FASTQ linting for early validation with FQ/LINT
  • #209 Add MULTIQC SAV support
  • #210 Added kraken2 subworkflow
  • #212 Add CheckQC module
  • #218 kraken2 is run on subsampled data if available
  • #226 Add pipeline level stub tests
  • #228 Update all modules/subworkflows

Fixed

  • #216 Fixed meta.id that resulted in all SEQFU_STATS processes with the same tag name
  • #224 Fix workflow output syntax for future Nextflow releases
  • #226 Fix parameter tools_bundle not accepting null for custom tool selection

Changed

  • #191 Back to dev
  • #192 Refactor the tools selection logic
  • #192 Removed bwamem2_index, bwamem2_mem, samtools_faidx and samtools_index from the list of tools as they can be inferred from downstream tools
  • #192 Removed params run_picard_collecthsmetrics and add picard_collecthsmetrics to the list of tools
  • #192 Removed seqtk_sample from the list of tools as it can be inferred from params.sample_size
  • #205 document how to add a tool to tool selection and how to use tool selection
  • #215 Update all modules
  • #216 Split out and simplify tests
  • #220 Workflow output for MultiQC
  • #221 Workflow output for checkQC, Fastp, fastp, fastqe, fastqscreen, picard_collecthsmetrics, picard_collectmultiplemetrics, rundirparser, seqfu
  • #222 Workflow output for fq/lint, kraken2, krona, toulligqc
  • #223 Workflow output for the rest of the pipeline

Dependencies

Dependency Old version New version
checkQC 4.1.0
fastp 1.1.0
fastqe 0.5.2
fq/lint 0.12.0
htslib 1.22.1 1.23.1
kraken2 2.1.6
krona 2.8.1
multiqcsav 0.2.0
samtools 1.22.1 1.23.1
toulligqc 2.8.4
tar 1.34

Deprecated

  • #213 Removed sort_bam params as we always need sorted BAM files for the QC_BAM subworkflow

1.0.1 - Penelope Ruth "Penny" Gadget

Added

Fixed

  • #182 Keep modules diff to a minimum
  • #183 Fix tag collision warning message that was actually printed for every tag
  • #185 No failure when no fasta file is provided
  • #189, #190 Fix GHA from #186

Changed

  • #180 Add Zenodo record
  • #181 Back to dev
  • #184 Display the tag name as ID in the MULTIQC_PER_TAG task
  • #186 Remove hook_url from the pipeline configuration, cftools#4051
  • #187 Prepare release 1.0.1

Dependencies

Deprecated

1.0.0 - Inspector Gadget

Initial release of nf-core/seqinspector, created with the nf-core template.

Added

  • #2 Input workflow and schema definition
  • #13 Generate reports per run, per project and per lane
  • #20 Use tags to generate group reports
  • #50 Add an optional subsampling step
  • #51 Add nf-test to CI
  • #53, #64 Add FastQ-Screen database multiplexing and limit scope of nf-test in CI
  • #56 Added SeqFu stats module
  • #63 Contribution guidelines added about displaying results for new tools
  • #68 Add tool selector
  • #75 Set up nft-utils
  • #96 Added missing citations to citation tool
  • #100 Added official logos
  • #103 Configure full-tests
  • #106 Parse rundir metadata
  • #108 Test data validation (#94)
  • #108 Update lists of default steps in the pipeline (#86)
  • #110 Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns
  • #111 Short summary of seqinspector in README.md (#84)
  • #127 Added alignment tools - bwamem2 - index and mem
  • #128 Added Picard tools - Collect Multiple Mterics to collect QC metrics
  • #132 Added a bwamem2 index params for faster output
  • #135 Added index section to MultiQC reports to facilitate report navigation (#125)
  • #148 Add Tubemap
  • #151 Added a prepare_genome subworkflow to handle bwamem2 indexing
  • #156 Added relative sample_size and warning when a sample has less reads than desired sample_size
  • #159 Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
  • #162 Add tests for prepare_genome subworkflow
  • #168 Add contributors list
  • #168 Add logo to the pipeline logo
  • #174 Add nf-core-utils 0.4.0
  • #180 Add Zenodo record

Fixed

  • #71 FASTQSCREEN does not fail when multiple reads are provided
  • #77 Use a params for fastqscreen csv file, and not the hardcoded example one
  • #99 Fix group reports for paired reads
  • #107 Put SeqFU-stats section reports together
  • #108 Go through and validate test data (#94)
  • #112 Making fastq_screen_references value to use parentDir
  • #121 Cleanup sample naming for MultiQC report (#105)
  • #150 Fix pipeline linting issues
  • #162 Fix bugs in qc_bam and prepare_genome subworkflows and add tests
  • #163 Run fastqscreen with subsampled data if available
  • #167 RunDirParser is now skipped if no Run Directory information is available
  • #169 Rescue missing versions from PREPARE_GENOME subworkflow
  • #171 Rescue number of tasks in the pipeline level tests
  • #172 More complete conda environment for rundir parser
  • #173 Fix warning message for tag name collision
  • #174 Fix null message when no rundir information is available
  • #175 Fix conda setup in CI
  • #178 Fix nextflow schema
  • #178 Fix links in documentation

Changed

  • #15 Template update for nf-core/tools v2.14.1
  • #26, #49 Template update for nf-core/tools v3.0.2
  • #69 Template update for nf-core/tools v3.1.0
  • #72 Template update for nf-core/tools v3.1.2dev0
  • #74 Template update for nf-core/tools v3.2.0
  • #114 Update CI
  • #133 Template update for nf-core/tools v3.4.1
  • #144 Template update for nf-core/tools v3.5.1
  • #145 Remove outdated comments
  • #148, #152, #153 Update documentation
  • #158 Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
  • #164 Refactor local subworkflow and pipeline tests
  • #168 Adhere to strict syntax
  • #169 Prepare release 1.0.0
  • #173 Improve documentation
  • #174 Refactor tests
  • #174 More strict syntax
  • #174 No params included in workflows
  • #175 Update all modules and migrate the whole pipeline to using topic versions
  • #176 No modules binaries
  • #177 Remove non used modules
  • #177 Move PREPARE_GENOME to the root main.nf script
  • #179 Set minimal Nextflow version to 24.10.2

Dependencies

  • #116 Update MultiQC to 1.28
  • #174 Update nf-schema to 2.6.1

Deprecated