v1.3

• Add an external config file to adapt to the cluster (with 2 examples)
• remove DRMAA dependency

v1.1

Change Snakemake version to fit recent Apptainer version on the clusters.

v1.0

• Add transcriptome pseudo-mapping with Salmon
• Move to Singularity image instead of Conda env
• Add single-end test data
• Update most tools
• Improve reporting
• Move several functions to edc_workflows.py, simplify main sh script for readability
• Add scripts for genome indexing

Version v0.7

• Add the possibility to download FASTQ files from SRA.
• Add configuration checker.
• Check/lock if the workflow is already running.
• Change .snakemake/conda localisation -> home

Bug fixes:

• Correct bug merging summaries

Version v0.6.2

Snakemake update.
Invert color for expression heatmaps.
Add iPOP-UP sbatch file.
Start from count tables
-A option for IFB
Copy conf file temporary
Bug fixes:

• Error in TEcount with stranded = no

Version v0.6

Merge with the dev repo.

• Add repeat analysis (also in the test dataset)
• Split big bam files and merge resulting count tables
• Improve efficiency on the cluster
• Measure disk usage
• Add options for featureCounts and HTseq

Version v0.5

(26/02/2021)

• Add a report in html format
• Add Glimma interactive plots
• Add a test dataset
• Improve resource usage

Version v0.4

v0.4 (25/09/20)

• Allow to start from count tables, including PCA and sample distances
• Add STAR 2.7.5a (including counter)
• Add script to generate STAR index
• Modify multiQC call to include mapping and counting QC
• Change names of the result folders
• Correct empty log for initial QC
• Remove plotscale library
• Export errors in the main log
• Save the configuration files for each run
• Export PCA and sample distances for each pair of DEA

Version v0.3

v0.3 (28/07)

• Adaptation to RPBS cluster
• Work with both TRIM3: no and TRIM3: "no"
• Correction bug in ht-seq rules
• Modification of module loading
• Modification job names

v0.2

v0.2 (03/07)

• update all the tools (22/06/2020)
• separate output folder for DESeq2 and edgeR
• Add DESeq2Report (for both DESeq2 and edgeR)
• Add featureCounts
• MultiQC after counting