CHANGELOG.md

1.5.4

Features

• fair_bowtie2_mapping up to 4.1.3

1.5.3

Features:

• fair_bowtie2_mapping up to 4.1.2

1.5.2

Features:

• Better resources reservation
• snakemake-wrappers up to 3.13.7
• fair_bowtie2_mapping up to 4.1.0
• Allow local pipeline search
• Allow local snakemake-wrappers

Fixes:

• Format error

1.5.1

Features:

• fair_bowtie2_mapping up to 3.5.2
• fair_genome_indexer up to 3.8.1
• Memory / time reservations

1.5.0

Features:

• Split multi-allelic sites and left-normalize
• Automatically filter passing variants
• Support of tumor/normal-pairs calling

1.4.2

Features:

• More time for Mutect2 rule

1.4.1

Features:

• fair_bowtie2_mapping update to 3.3.3
• fair_fastqc_multiqc update to 2.2.7

1.4.0

Features:

• Snakemake wrappers up to 3.7.0
• fair_fastqc_multiqc up to version 2.2.6
• fair_bowtie2_mapping up to version 3.3.2
• fair_genome_indexer up to version 3.4.4

1.3.0

Features:

• Handle somatic calling if possible
• Snakemake wrappers up to version 3.5.2
• fair_bowtie2_mapping up to version 3.3.0
• fair_fastqc_multiqc up to version 2.2.1
• fair_genome_indexer up to version 3.3.0
• Configuration keys are all optional

1.2.0

Features:

• Snakemake wrappers up to version 3.5.0
• fair_bowtie2_mapping up to version 3.2.0
• fair_fastqc_multiqc up to version 2.1.2
• fair_genome_indexer up to version 3.2.2
• SnpEff + SnpSift basic annotations
• Pipeline containerized

1.1.1

Fix:

• missing Log/benchmark

1.1.0

Features:

• temp, log, and benchmark paths rebuild
• rule names changed to follow between-workflows trace
• use of lookup instead of hand-made function
• Relies on fair_genome_indexer version 3.1.4
• Relies on fair_bowtie2_mapping version 3.1.0
• Relies on fair_fastqc_multiqc version 2.0.3
• MultiQC now holds only one {species}.{build}.{release}

Fixes:

• Documentation update

1.0.0

Features:

• Snakemake v8+ compatible
• Snakemake-wrappers
• Relies on fair_genome_indexer version 3.0.0
• Relies on fair_bowtie2_mapping version 3.0.1
• Deployable workflow with integration tests on Github