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v.1.1.0 - 2021-05-11
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@KevinMenden KevinMenden released this 15 Jun 12:46
· 1253 commits to master since this release
1.1.0
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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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