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Releases: nf-core/smrnaseq

v.1.1.0 - 2021-05-11

15 Jun 12:46
@KevinMenden KevinMenden
1.1.0
03333bf
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v.1.1.0 - 2021-05-11

v1.1.0 - 2021-05-11

Major changes

⚠️ Breaking changes!

This release contains several major (potentially breaking) changes:

  • The main input parameter has been changed from --reads to --input to standardize the pipeline with other nf-core pipelines
  • All parameter documentation has moved into a new nextflow_schema.json file
  • A lib folder with groovy helper classes has been added to the pipeline. This includes validation of input parameters using the schema defined in the nextflow_schema.json file

General improvements

  • remove spaces in genome headers and replace special nt by N in hairpin file for mirdeep2 to work. [#69]
  • Accept custom genome and remove non-canonical letters in the genome. Thanks to @sdjebali. Follow up from [#63]
  • Fix error when only one sample is in the input [#31]
  • Made CamelCase pipeline parameters snake_case and lower case
    • clip_R1 -> clip_r1
    • three_prime_clip_R1 -> three_prime_clip_r1
    • saveReference -> save_reference
    • skipQC -> skip_qc
    • skipFastqc -> skip_fastqc
    • skipMultiqc -> skip_multiqc
  • Update with the latest TEMPLATE version for nf-core 1.12.1
  • Update conda environment with new packages and updates
  • Added --protocol custom to allow custom adapter trimming modes [#41]]
  • Fix error when UMI is on the reads header: [#35]
  • Updated params.mirtrace_species to be properly initialised when using --genome, for all iGenomes species
  • Made params.mature and params.hairpin default to miRBase FTP URL so that the file is automatically downloaded if not provided
  • Allow .fa or .fa.gz files for mature and hairpin FASTA files.
  • Add full-size benchmark / test dataset to run on AWS for each release (see test_full.config)
  • Add -f flag to gunzip commands to deal with soft-links
  • Add --mirtrace_protocol parameter to allow for more flexible selection of this parameter
  • Added --trim_galore_max_length option [#77]
  • Solved memory usage issue for mirtrace in the main process and in the get_software_versions process [#68]
  • Removed logging of single_end parameter and added missing parameters to schema and config files
  • Added "custom" as option for --protocol in the nextflow_schema.json

Packaged software updates

  • fastqc=0.11.8 -> 0.11.9
  • trim-galore=0.6.3 -> 0.6.5
  • bowtie=1.2.2 -> 1.2.3
  • multiqc=1.7 -> 1.9
  • mirtop=0.4.22 -> 0.4.23
  • seqcluster=1.2.5 -> 1.2.7
  • htseq=0.11.2 -> 0.11.3
  • fastx_toolkit=0.0.14 -> 0.0.14
  • seqkit=0.10.1 -> 0.12.0
  • mirtrace=1.0.0 -> 1.0.1
  • Added conda-forge::python=3.7.3
  • Added conda-forge::markdown=3.1.1
  • Added conda-forge::pymdown-extensions=6.0
  • Added conda-forge::pygments=2.5.2
  • Removed conda-forge::r-markdown=1.0
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nf-core/smrnaseq v1.0.0

21 Sep 09:10
@apeltzer apeltzer
1.0.0
28f3418
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nf-core/smrnaseq v1.0.0

v1.0.0 - 2019-09-21

  • 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

Other

  • Add "protocol" with pre-defined settings
  • Add miRTrace in the pipeline.
  • 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 center in BAM file.

Dependency Updates

  • 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
Assets 2
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