3.0.1

Features:

• Genome schema validation update

Fixes:

• Report testing removed as long as TBD issue is opened
• Do not download un-necessary reference files anymore

3.0.0

Breaking change: Non canonical chromosomes removed by default

Features:

• fair_genome_indexer update to 3.0.0
• snakemake-wrappers updated to v3.3.3
• snakemake github action updated to 1.25.1
• Documentation update

Fix:

• Wrong parameters passed to MultiQC when importing pipeline with no parameters

Documentation:

• Pipeline description updated
• Usage generalized
• Gustave Roussy users have a dedicated usage section

2.3.0

Features:

• Include fastqc/multiqc as a module
• Rename meta-wrapper rules to indetify them
• Define generic genomes
• Add configuration keys
• Add MultiQC report label

Fix:

• Mat&Met typos
• Multiqc report missing tools
• test Makefile update for Snakemake 8+

2.2.8

Features:

• Reduce time and memory reservations
• Snakemake-wrappers up to 3.3.3
• Snakemake 8+ compatibility

Fix:

• csv.Sniffer getting too much data

2.2.7

Features:

• Snakemake-wrappers update
• Linter compliance

2.2.6

Features:

• FastQC in addition to pre-trimming fastp

Fix:

• Fix wrong reference linking in picard

2.2.5

Features:

• Update fair_genome_indexer to version 2.3.0
• Samtools stats added to report

Fix:

• Report main page too large
• Fix error removing Bowtie2 QC from MultiQC report
• Fix error making fastp reports non reachable in MultiQC

2.2.4

Features:

• reduce size of configuration provided to fair_genome_indexer
• Include Bowtie2 metrics to MultiQC report

Fix:

• Fix picard metrics extra parameter missing
• genomes not found while importing workflow as module
• Bowtie2-build now takes fasta, if fasta is provided and no bowtie2 index is provided
• Single-end error when mixed single-ended/pair-ended samples were mixed in design

2.2.3

Features:

• Conditionally load fair_genome_indexer
• Let user provide annotation files

2.2.2

Features:

• Documentation update
• Rename loaded rules from fair_genome_indexer rule to indetify them