v0.4.1

updated subread version from v1.6.0 to v1.6.2

Fixed subread error when >70 samples are used.

Release v0.4.0

This new release fix a few issues and adds a new functionality:

• fix issue with the mapping_summary.csv that had long column names with the directory and also an unnecessary index (0,1,2, etc.).
• add a switch in config/config.yaml to keep the temporary working directory or not. This can be useful when one wants to keep the trimmed files for instance.

Release v0.3.8

This release adds the "--genomeChrBinNbits" parameter to STAR for the genome index generation step. It helps the memory usage when genomes are long and fragmented in many scaffolds.

Release v0.3.7

This release has:

• An option to count multimapping reads (turned "off" by default)
• Scaling is not done if only one sample is given.

Release v0.3.5

Add multiQC for quality check report of mRNA-seq reads.

Release v0.3.4

This release fix the bug related to the trimming function.

Version 0.3.1

This release creates five different outputs from mRNA-seq reads:

• .html reports of the mRNA-seq fastq quality checks.
• .bam mapping files sorted by chromosomal coordinates.
• mapping_summary.tsv, a summarised mapping report for all samples.
• raw_counts.tsv, a table comprising the raw unscaled count values for genes in the provided GTF annotation file.
• scaled_counts.tsv, a table comprising the scaled count values as given by DESeq2 for genes in the provided GTF annotation file.

Nb: the .tsv extension stands for tabulated separated values.

Version 0.3.0

This release contains a Dockerfile used to build a Docker image that can be used to run the pipeline in a Docker container.