- Add figures to output documentation
- Add samtools stats for genome alignments
- Add seqkit and remove razers
- Add mirtop and razers tools
- Adapt code and docs to nf-core template
- Update tools and Dockerfile/Singularity to match current template
- openjdk 8.0.144 -> 11.0.1
- fastqc 0.11.7 -> 0.11.8
- trim-galore 0.5.0 -> 0.6.2
- bioconductor-edger 3.20.7 -> 3.26.0
- bioconductor-limma 3.34.9 -> 3.40.0
- conda-forge::r-data.table 1.11.4 -> 1.12.2
- conda-forge::r-gplots 3.0.1 -> 3.0.1.1
- conda-forge::r-r.methodss3 1.7.1 -> 1.7.1
- htseq 0.9.1 -> 0.11.2
- r-markdown 0.9
- Added mirtop 0.4.18a
- Removed razers3 3.5.3
- Added seqkit 0.10.1-1
- Added seqcluster 1.2.5
- conda-forge::r-base=3.5.1 -> 3.6.1
- conda-forge::r-statmod=1.4.30 -> 1.4.32
- conda-forge::r-markdown=0.9 -> 1.0
- trim-galore=0.6.2 -> 0.6.3
- mirtop=0.4.18a -> 0.4.22
- bioconductor-edger=3.26.0 -> 3.26.5
- bioconductor-limma=3.40.0 -> 3.40.2
1.0 - 2019-01-10
- Add "protocol" with pre-defined settings
- Add miRTrace in the pipeline.
- Software updates: multiqc 1.6 to 1.7.
1.0 - 2018-08-06
- Switch from SciLifeLab/NGI-smRNAseq to nf-core/smrnaseq.
- Use Bowtie 1 instead of Bowtie 2 for the alignment to host reference genome.
- Add option for sequencing centre in BAM file.
- Software updates: trim-galore 0.4.5 to 0.5.0; samtools 1.8 to 1.9; multiqc 1.5 to 1.6.