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Recent Releases of fair_genome_indexer

fair_genome_indexer - 3.10.0

Features:

  • Compute genome statistics (non-n-base genome size, intron lengths, ...)

- Python
Published by tdayris 9 months ago

fair_genome_indexer - 3.9.8

Features:

  • Snakemake-wrappers update

Fix:

  • Ensure non conventionnal contigs are removed

- Python
Published by tdayris 9 months ago

fair_genome_indexer - 3.9.7

Features:

  • Snakemake-wrappers update

- Python
Published by tdayris 12 months ago

fair_genome_indexer - 3.9.6

Features:

  • Automatic STAR memory specification

- Python
Published by tdayris about 1 year ago

fair_genome_indexer - 3.9.5

Features

  • Snakemake wrappers up to 5.6.0
  • Agat + Bash update

- Python
Published by tdayris about 1 year ago

fair_genome_indexer - 3.9.4

Features:

  • Snakemake wrappers up to 5.5.0
  • tasks updated
  • Agat update

- Python
Published by tdayris about 1 year ago

fair_genome_indexer - 3.9.3

Features:

  • Easy snakemake-wrappers update
  • Easy conda envs update
  • New testing pipeline with additional format checks
  • Snakemake wrappers update to 5.3.0
  • Agat, python, and Snakemake environments update

Doc:

  • Citation cff file

- Python
Published by tdayris about 1 year ago

fair_genome_indexer - 3.9.2

Features:

  • Environement pins

Documentation

  • Update for the configuration section

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.9.0

Features:

  • Fasta to 2bit
  • Snakemake-wrappers up to 4.5.0

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.8.1

Features:

  • Memory/Time reservation adjusted

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.8.0

Features:

  • STAR indexes
  • Salmon index
  • Genepred file formats
  • Re-use of indexed files

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.7.0

Fix:

  • Blacklist download link updated
  • Agat temporary file handled

Features:

  • Include bowtie2 indexes

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.6.2

Fix:

  • Protect against nan values in genome queries

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.6.1

Features:

  • Documentation udpate

Fix:

  • blacklist merge fixed

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.6.0

Features:

  • Separate resources among subdirectories holding genome names
  • Snakemake up to 8.13.0
  • Snakemake wrappers up to 3.12.0

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.5.0

Features:

  • Changes in configuration: parameters now holds the name of the rule they refer to
  • Log, Benchmarks, and temp files now point to a directory named from their rule name
  • Reservation made according to Gustave Roussy's Flamingo tests on Ensembl's GRCh38
  • snakemake-wrappers update to 3.10.2

- Python
Published by tdayris over 1 year ago

fair_genome_indexer - 3.4.4

Features:

  • Documentation udpate

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.4.3

Features:

  • Schema update
  • Cleaning

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.4.2

Features:

  • Use human readable functions to replace raw lookups
  • snakemake-wrappers update to 3.7.0

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.4.0

Features:

  • User-provided files are used more regularly
  • Slurm resources more closely related to homosapiens and musmusculus requirements

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.3.1

Features:

  • Fix wildcard error on non-human organisms

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.3.0

Features:

  • Configuration keys are all optional
  • Snakemake-wrapper up to version 3.5.2

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.2.2

Features:

  • While importing this pipeline and many others to large workflows, parmspace was too large. It has been splitted with clear pipeline names in it
  • UCSC genePred format
  • Tests are now containerized

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.2.0

Features:

  • Snakemake wrappers update to 3.4.1
  • Full containerization

- Python
Published by tdayris almost 2 years ago

fair_genome_indexer - 3.1.4

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

Fixes:

  • All wget commands lookup in configuration for optional parameters

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 3.1.2

Features:

  • Partition handled in resources for Gustave Roussy's cluster only.

Fixes:

  • Badges fixed

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 3.1.1

Features:

  • Raise snakemake validation up to 8.1+

Fixes

  • Latest changes raises the snakemake requirements up to v8.1+
  • rsync was added to the bash environment

Documentation

  • Users of Gustave Roussy's computing cluster (Flamingo) have a new environment

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 3.1.0

Features:

  • Agat jobs now reserve more time to get rid of OOT errors
  • Skip agat-filter-from-attribute-value if no parameters is provided by user with branch
  • Check if species, build and release are empty. Do not try to download anything in that case.
  • snakemake-wrappers update to version v3.3.6 leading to both Samtools and Tabix update.
  • Use of lookup rather than hand-made parsing
  • Append pipeline name to all rule names in order to keep rule origin in future import, without breaking inner rule inheritence
  • timestamp ignored for genome indexes to avoid cluster touch issues
  • default ensembl-release set to 111

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 3.0.0

Breaking change: Non canonical chromosomes removed by default

Features:

  • pyfaidx optionally filters non-canonical chromosomes in fasta
  • agat filters NA TSL in GTF
  • bedtools filters non-canonical chromosomes in bed
  • bcftools filters non-canonical chromosomes in vcf
  • tabix index of filtered known variants
  • remove rules subdirectories

Fixes:

  • csv.Sniffer having too much data
  • Missing tests added

Documentation:

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

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 2.3.2

Features:

  • Snakemake-wrappers up to 3.3.3
  • Snakemake 8+ compatibility
  • main environment update

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 2.3.1

Features:

  • Memory/Time/tmp reservation for each rule, with attempt
  • Tests on Flamingo (Gustave Roussy's computing cluster)

Fix:

  • Agat logs overlapping
  • snakemake-wrappers version update to 3.2.0
  • format error on latest python/snakemake

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 2.3.0

Feature:

  • Pyroe id-to-name

Fix:

  • Report main page too large

- Python
Published by tdayris about 2 years ago

fair_genome_indexer - 2.2.0

Features:

  • Download ensembl-variations
  • Fix common ensembl format errors in GTF files
  • Update to Snakemake-Wrappers version 3.0.0
  • General report available

Fix:

  • Snakemake workflow compliance
  • fix target rules not returning GTF correctly

- Python
Published by tdayris over 2 years ago

fair_genome_indexer - 2.1.0

Features:

  • Download ensembl-variations

Fix:

  • Snakemake workflow compliance

- Python
Published by tdayris over 2 years ago

fair_genome_indexer - 2.0.2

Features:

  • linter: add log/benchmark to target rule

- Python
Published by tdayris over 2 years ago

fair_genome_indexer - 2.0.1

Features:

  • Removed useless files and links
  • Moved tests to .test accordingly to snakemake-workflow practices.

- Python
Published by tdayris over 2 years ago

fair_genome_indexer - 2.0.0

Important:

  • pipeline now requires snakemake >= 7.29.0

Features:

  • add benchmark directory
  • add workflow profile (requires snakemake >= 7.29.0)
  • tests directories are now included in .gitignore
  • Snakemake-workflow-catalog compliance

Fixes:

  • KeyError in blacklists while requesting wrong combination of genome build and releases

- Python
Published by tdayris over 2 years ago

fair_genome_indexer - 1.0.0

Initial release.

Features

  • Download and index a fasta sequence file (both DNA and cDNA)
  • Download a GTF annotation file
  • Download known blacklist regions for human and mouse genomes

- Python
Published by tdayris over 2 years ago