CHANGELOG.md

4.4.2

Features:

• Snakemake-wrappers update to 5.6.0
• fair_genome_indexer update
• fair_fastqc_multiqc update
• Reservations update

4.4.1

Features:

• Use of wrapper's version of Sex.DetERRmine
• Snakemake-wrappers update to 5.5.0
• Tasks update

Fix:

• Sex.DetERRmine used only on human and mice

4.4.0

Features:

• Snakemake-wrappers update to 5.3.0
• MTNucRatioCalculator added to QC
• Easy snakemake-wrappers update
• Easy conda envs update
• New testing pipeline with additional format checks

Doc:

• Citation cff file added

4.3.1

Features:

• Snakemake-wrappers up to 4.6.0

Documentation:

• Update in the configuration section

4.3.0

Features:

• Mosdepth included in QC

4.2.0

Features:

• Samtools idxstats included

Fixes:

• Deeptools alignment sieve producing non position-sorted bams

4.1.3

Features:

• bt2 index explicit

4.1.2

Features:

• Reduce fastp threads

4.1.1

Features:

• Allow local snakemake wrappers
• Allow local modules

4.1.0

Features:

• Fastp output compressed

4.0.0

Features:

• Deeptools alignment sieve (on params/make_sieve set to true)
• snakemake_wrappers up to 3.13.7

3.5.2

Features:

• fair_genome_indexer up to 3.8.1
• Memory / Time reservations

3.5.1

Features:

• fair_genome_indexer up to 3.8.0
• fair_fastqc_multiqc up to 2.3.5

3.5.0

Features:

• fair_genome_indexer up to 3.7.0
• fair_fastqc_multiqc up to 2.3.4

Documentation:

• Fix links

3.4.1

Features:

• Better reservations

3.4.0

Features:

• Fix benchmark IO for rseqc bamstat
• Use of wrappers for ngsderive
• tmp/logs/benchmark hold rulenames
• fair_fastqc_multiqc and fair_genome_indexer updates
• Pipeline can now localy import sub-modules

3.3.3

Features:

• fair_fastqc_multiqc update to 2.2.7

3.3.2

Features:

• Use human readable functions to replace raw lookups
• Documentation update

3.3.1

Features:

• fair_genome_indexer update to 3.4.0
• fair_fastqc_multiqc update to 2.2.3
• snakemake-wrappers update to 3.7.0

3.3.0

Featues:

• All keys in configuration are now optional
• Snakemake wrappers up to version 3.5.0

Documentation:

• Pipeline display update

3.2.0

Features:

• Snakemake-wrappers update to 3.5.0
• MultiQC configurations
• RSeQC: bamstat, read_distribution, read_gc, infer_experiment, and read_duplication
• Goleft: indexcov
• ngsderive: strandedness, instrument, readlen, and encoding

3.1.1

Fix:

• MultiQC mapping report now holds only the samples belonging to a common {species}.{build}.{release}
• Readme points to the right snakemake version

3.1.0

Update to Snakemake v8+

Features:

• Usage updated
• DAG as ascii art
• tempfiles, logs and benchmarks paths reorganized:
  • tmp/fair_fastqc_multiqc/{rule_name}/{wildcards}.{extension}
  • log/fair_fastqc_multiqc/{rule_name}/{wildcards}.log
  • benchmark/fair_fastqc_multiqc/{rule_name}/{wildcards}.tsv
• use of lookup and collect rather than hand made functions
• All keys in configuration must be present in configuration file

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 up to 3.2.0

Fix:

• linter-error

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

2.2.1

Features:

• Protect bam output
• Speed-up with wildcards constraints
• Speed-up Picard with BAI inclusion in input files
• Changed output directory order

Fix:

• snakemake wrappers version fixed

2.2.0

Features

• fastp reports included in snakemake report
• fair_genome_indexer pipeline version updated to 2.2.0
• snakemake wrappers version updated to v3.0.0
• Description of expected results with directoy architecture

2.1.1

Features

• fair_genome_indexer pipeline update

2.1.0

Features:

• Add report texts

Documentation

• Fastp citation

2.0.0

Features:

• Fastp-trimming (reports included in MultiQC)

1.0.0

Features:

• Download-index reference genome if missing
• Build bowtie2-index if missing
• Align reads
• Perform post-mapping QC with picard and aggregate reports with MultiQC