fair_bowtie2_mapping - 4.4.6

Features

• Remove default fastq_screen file
• Snakemake wrappers update to 5.8.3
• fairgenomeindexer update to 3.9.7
• fairfastqcmultiqc update to 2.5.5

- Python
Published by tdayris 12 months ago

fair_bowtie2_mapping - 4.4.2

Features:

• Snakemake-wrappers update to 5.6.0
• fairgenomeindexer update
• fairfastqcmultiqc update
• Reservations update

- Python
Published by tdayris about 1 year ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 1 year ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 1 year ago

fair_bowtie2_mapping - 4.3.1

Features:

• Snakemake-wrappers up to 4.6.0

Documentation:

• Update in the configuration section

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 4.2.0

Features:

• Samtools idxstats included

Fixes:

• Deeptools alignment sieve producing non position-sorted bams

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 4.1.3

Features:

• Reduce fastp threads

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 4.1.2

Features:

• Fastp threads reduced

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 4.1.1

Features:

• Allow local snakemake wrappers
• Allow local modules

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 4.1.0

Features:

• Fastp output compressed

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 4.0.0

Features:

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

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 3.5.2

Features:

• fairgenomeindexer up to 3.8.1
• Memory / Time reservations

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 3.5.1

Features:

• fairgenomeindexer up to 3.8.0
• fairfastqcmultiqc up to 2.3.5

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 3.5.0

Features:

• fairgenomeindexer up to 3.7.0
• fairfastqcmultiqc up to 2.3.4

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 3.4.0

Features:

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

- Python
Published by tdayris over 1 year ago

fair_bowtie2_mapping - 3.3.3

Features:

• fairfastqcmultiqc update to 2.2.7

- Python
Published by tdayris almost 2 years ago

fair_bowtie2_mapping - 3.3.2

Features:

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

- Python
Published by tdayris almost 2 years ago

fair_bowtie2_mapping - 3.3.1

Features:

• fairgenomeindexer update to 3.4.0
• fairfastqcmultiqc update to 2.2.3
• snakemake-wrappers update to 3.7.0

- Python
Published by tdayris almost 2 years ago

fair_bowtie2_mapping - 3.3.0

Featues:

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

- Python
Published by tdayris almost 2 years ago

fair_bowtie2_mapping - 3.2.0

Features:

• Snakemake-wrappers update to 3.5.0
• MultiQC configurations
• RSeQC: bamstat, readdistribution, readgc, inferexperiment, and readduplication
• Goleft: indexcov
• ngsderive: strandedness, instrument, readlen, and encoding

- Python
Published by tdayris almost 2 years ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 3.1.0

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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 3.0.0

Breaking change: Non canonical chromosomes removed by default

Features:

• fairgenomeindexer 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 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+

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.7

Features:

• Snakemake-wrappers update
• Linter compliance

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.6

Features:

• FastQC in addition to pre-trimming fastp

Fix:

• Fix wrong reference linking in picard

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.5

Features:

• Update fairgenomeindexer 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.4

Features:

• reduce size of configuration provided to fairgenomeindexer
• 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.3

Features:

• Conditionally load fairgenomeindexer
• Let user provide annotation files

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.2

Features:

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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.2.0

Features

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

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 2.1.0

Features:

• Add report texts
• Fastp-trimming (reports included in MultiQC)

Documentation

• Fastp citation

- Python
Published by tdayris about 2 years ago

fair_bowtie2_mapping - 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

- Python
Published by tdayris about 2 years ago