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Recent Releases of fair_fastqc_multiqc

fair_fastqc_multiqc - 2.5.5

Features:

  • Snakemake-wrappers update to 5.8.3
  • fairgenomeindexer update to 3.9.7
  • Remove fastq_screen config file

- Python
Published by tdayris 12 months ago

fair_fastqc_multiqc - 2.5.4

Features:

  • Default configuration update

- Python
Published by tdayris 12 months ago

fair_fastqc_multiqc - 2.5.2

Features:

  • Only raise warning on untouchable files
  • Snakemake wrappers update to 5.6.0
  • fairgenomeindexer update to 3.9.5

- Python
Published by tdayris about 1 year ago

fair_fastqc_multiqc - 2.5.1

Fix:

  • Allow fastq to be untouchable from current node (iRODS, cold-storage, ...)

- Python
Published by tdayris about 1 year ago

fair_fastqc_multiqc - 2.5.0

Features:

  • Seqtk added to check fastq files

- Python
Published by tdayris about 1 year ago

fair_fastqc_multiqc - 2.4.2

Features:

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

Docs:

  • Citation cff file added

- Python
Published by tdayris about 1 year ago

fair_fastqc_multiqc - 2.4.1

Features:

  • More clear error on when a source file does not exists

Documentation:

  • Report update

- Python
Published by tdayris about 1 year ago

fair_fastqc_multiqc - 2.4.0

2.4.0

Features:

  • fastqinfo used to validate and gather quality metrics over fastq files and maximum theoretical coverage.
  • Seqkit used to gather quality metrics over fastq files
  • fastq_utils used to gather quality metrics over fastq files

Fix:

  • Input file concatenation edge case

Documentation:

  • Update for the configuration section

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.3.6

Features:

  • Snakemake-wrappers update to 4.5.0

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.3.5

Fix:

  • fastq screen parameters

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.3.4

Feature:

  • drop compresison dependencies

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.3.3

Feature:

  • drop dependency

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.3.2

Fix

  • Blacklist fix in fairgenomeindexer

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.3.1

2.3.1

Features

  • Documentation udpate

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.8.0

Features

  • Update snakemake wrappers to 3.10.2
  • Report update
  • More readable tmp and logs

- Python
Published by tdayris over 1 year ago

fair_fastqc_multiqc - 2.2.7

Fix

  • Fix R2 copy issue

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.6

Features

  • Snakemake wrappers up to 3.7.0

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.5

Features: * Documentation update

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.4

Fix:

  • Since copies are done on node and not on login-node, the on_flamingo() flag is removed

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.3

Features:

  • symlink fully absolute
  • Do not run useless copy/symlinks before compression

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.2

Fix:

  • Missing packages in python environment used for copy
  • Fix FileNotFoundError in apptainer when using this pipeline as an external module
  • rsync syntax error

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.1

Fixes:

  • Json schema

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.2.0

Features

  • Configuration keys are all optional
  • Snakemake wrappers update to version 3.5.2

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.1.2

Features:

  • Configuration update

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.1.1

Fix:

  • Missing file

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.1.0

Features:

  • Snakemake wrappers updated to 3.4.1: including an exciting MultiQC update!
  • A dedicated MultiQC configuration file is created
  • Pipeline containerized

Fixes:

  • Documentation errors
  • Report typos

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.1.0

Features:

  • Snakemake wrappers updated to 3.4.0: including an exciting MultiQC update!
  • A dedicated MultiQC configuration file is created
  • Pipeline containerized

- Python
Published by tdayris almost 2 years ago

fair_fastqc_multiqc - 2.0.4

Features:

  • Debug logs in link_or_concat.py

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 2.0.3

Fixes:

  • AttributeError when empty lookup list is returned

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 2.0.2

Features:

  • Removed slurm partition function
  • Job reservation based on input file size
  • 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 to find configuration values
  • Dag as ascii-art

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 2.0.1

Features:

  • Add slurm_partition for snakemake plugin executor

Documentation

  • Usage updated

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 2.0.0

Snakemake v8.1+ required

Features

  • New QC: FastqScreen, available if, and only if a configuration file is provided.
  • Snakemake Wrappers update to 3.3.6
  • Github actions updated
  • Use of lookup and queries instead of hand-made samples.csv parsing
  • DAG available on readme

Known bugs

  • Report is unavailable as long as the TBD issue is opened on Snakemake

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 1.0.4

Features

  • More precise configuration file validation
  • Labed added to MultiQC to make it more noticable

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 1.0.3

Features

  • Hidden keys in documentation are now described
  • MultiQC report name changed in order to identify it more easily
  • Example report available
  • Disk usage reservation
  • Explicit time/memory reservation

Fixes

  • Documentation pointing to fastp and not fastqc
  • Typo in snakemake report main page

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 1.0.2

Fixes

  • csv.Sniffer having too much data to define delimiter

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 1.0.1

Features

  • Updated readme
  • Updated report content
  • Snakemake workflow catalog updates

- Python
Published by tdayris about 2 years ago

fair_fastqc_multiqc - 1.0.0

Features

  • Run FastQC on single/pair ended fastq files
  • Aggregate reports in MultiQC

Known bug

  • Using Snakemake 8.0.0+ the report is broken. Error is known.

- Python
Published by tdayris about 2 years ago