Skip to content

Latest commit

 

History

History
222 lines (125 loc) · 3.41 KB

CHANGELOG.md

File metadata and controls

222 lines (125 loc) · 3.41 KB
Raw

2.3.4

Feature:

  • drop compresison dependencies

2.3.3

Feature:

  • drop dependency

2.3.2

Fix

  • Blacklist fix in fair_genome_indexer

2.3.1

Features

  • Documentation udpate

2.3.0

Features

  • Snakemake updates now follow the updates from fair_genome_indexer
  • Improt functions and globals from fair_genome_indexer

2.2.8

Features

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

2.2.7

Fix

  • Fix R2 copy issue

2.2.6

Features

  • Snakemake wrappers up to 3.7.0

2.2.5

Features:

  • Documentation update

2.2.4

Features:

  • Documentation update
  • Use human readable functions rather than raw lookup
  • schemas update

2.2.3

Fix:

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

2.2.2

Fix:

  • symlink fully absolute

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

2.2.1

Fix

  • Json schema

2.2.0

Features

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

2.1.2

Features:

  • Changes in configuration

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

2.0.4

Features:

  • Debug logs in link_or_concat.py

2.0.3

Fixes:

  • AttributeError when empty lookup list is returned

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

Fixes:

  • Documentation error

2.0.1

Features:

  • Add slurm_partition for snakemake plugin executor

Documentation

  • Usage updated

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

1.0.4

Features

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

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

1.0.2

Fixes

  • csv.Sniffer having too much data to define delimiter

1.0.1

Features

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

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.