Release version 0.12.0

Latest dev version updated merged into the main branch contain the following updates

20: Bugfix: One sample was removed from the DE analysis in the final report by accident.
19: Barplot legends work now also, when no biotypes are provided in the referene annotation
18: Overall statistics split now noFeature and noFeature, but used for novel miRNA
17: SOme if-clauses added for more stable finalReport execusion
16: Some default resource allocations added
15: Bugfix, in getJoinedLoci minimum coverage was >, but it should have been >= to meet correct settings
14: Bugfix, that crashed finalReport in case only two samples were used in the pipeline
13: tOption is now also used in the final report
12: Missing memory allocation in one rule was added.
11: Bugfix, server-config did not receive the project path, if not given explicitely in config file
10: Added samtools_nonTRNA_reads_phix_flagstats to default resource allocation
9: Added samtools_concatenated_reads_tRNA_flagstats to the dedicated resource allocations
8: Added featureCounts options to account for non-default gtf file in quantification (-t and -g options)
7: Additional server resources added to the server_config file
6: Option for DE testing with edgeR added
5: sampleInfo-file option added
4: Config allows now relatives PATHs and adjustes them tot eh current project folder
3: Parameter for minimum coverage for novel miRNA detection added
2: Quantification table for reference counts added
1: New dev branch, identical to 0.10

Stable release version 0.10

Included the previous dev-updates, quick release because of critical bugfix

0.9.*

3: Critical bugfix - Separate 3' and 5' adapter trimming was doing wrong
2: Added the option not to use any adapter trimming

Pipeline release version 0.8.1

Previous update 0.7.9 was not part of the last release 0.8.

Stable release version 0.8

Release version contains the previous dev-version changes:

8: Pipeline allows now separate 3' and 5' adapter trimming
7: Critical bugfix, seqkit rules reported suddenly non-zero exit errors
6: Case caught, when no novel genes are detected
5: Critical bugfix in the seqkit output
4: Path bug in final report fixed (after renaming not adjusted)
3: Resource allocations for a missing rule added
2: Some defaults server resource allocations adjusted
1: New dev branch opened

Stable release version 0.6

Latest release from the miRNA pipeline, including the following changes:

24: Structure in chapter 'Origin of reads' optimised
23: Resolution for the read summary figure adjusted
22: Bugfix for RPKm calculation in STAR protein coding expression values
21: hairpin_species quantification table is exported to the QUANTIFICATION folder
20: hairpin quantification table is exported to the QUANTIFICATION folder
19: mature_species quantification table is exported to the QUANTIFICATION folder
18: mature quantification table is exported to the QUANTIFICATION folder
17: tRNA quantification table is exported to the QUANTIFICATION folder
16: Bugfix for mirna-species filtering (caused that not all miRNAs were quantified)
15: Subparagraph added for novel clustering (missing linebreak added)
14: stdout and stderr are now redirected to CUTADAPT log files
13: STAR indices are not created in groups anymore
12: Quantification is now also grouped
11: Preprocessing is done in a single group now
10: QC rules are combined into two groups, fastqc and multiqc
9: The alignment module has now only two groups, bowtie_alignment and star_alignment
8: All rules in the decontamination module are now grouped together
7: Bug in the concatenation file selection fixed
6: Concatenating figure displays now only integers on the y-axis
5: Changed input to a single samplesheet format allowing flexible file names
4: Moved graphs into subparagraphs for better report readability
3: tRNA quantification, clustering and PCA were added to the final report
2: Colours in the report are adjusted to new colouring scheme
1: tRNA reads are now sorted, indexed and the idxstats are calculated (effectively tRNAs are quantified now)

Pipeline release version 0.4

First stable release version of this pipeline