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CHANGELOG.md

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Changelog

v2.6.0

  • remove indexing from pipeline, expect pre-made index.
  • assume now that partial decoy index or txtome index is used, hence lower memory for quant to 8GB

v2.5.2

  • check in tximport process whether there is a mismatch between tx2gene file and quant.sf identifiers that can be solved by using either of the ignoreTxVersion or ignoreAfterBar arguments of tximport(), and if so, do it automatically. This is relevant for Ensembl-based annotations where the GTF file often does not contain transcript versions (like ENSTXXXX.[digit]) but the transcriptome fasta headers do. This then creates a mismatch between tx2gene and the quant.sf transcript names which is annoying. This check will compensate for it.
  • quant.sf files from salmon are now gzipped

v2.5.1

  • update container

v2.5

  • adapted the idea of the meta-map from nf-core for module inputs
  • merge samples with multiple fastq files prior to fastqc/quantification
  • robustified reading from samplesheet
  • modules that use fastq now read a [meta, reads] map that includes the information on libtype and single-end/paired-end
  • added a trimmer/seqtk module
  • all relevant modules now return a tuple with software versions and command lines that a dedicated process collects and publishes in a summary file at the end of the pipeline
  • updated container to v1.6.1
  • added CITATIONS.md
  • check if files in samplesheet exist

v2.4

  • moved samplesheet validation to a process
  • updated container
  • report command lines and software versions for salmon and tximport, and emit to publishDir

v2.3

  • use stageAs in fastqc and quant modules to deal with situation where several fastq files per sample have the same name (name collision)

v2.2a

  • add --skip_tximport flag

v2.2

  • updated software versions, see CONTAINERLOG.md
  • added a schema.version option to display the current pipeline version

v2.1

  • add native samplesheet validation, checking for existance of the fastq files, that technical replicates have same libtype, no mix of single/paired-end data and that header line of samplesheet is correct

v2.0

  • updated with nf_blank template
    • params validation with params listed in schema.nf
    • intro message with summary of all params upon startup of pipeline
    • validate minimal NF version
  • read fastq files via samplesheet
  • detect and automerge technical/lane replicates
  • added fastqc and multiqc
  • added a CI test for singularity
  • add tximport

phd_project_version

  • initial release