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CHANGELOG.md

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MPRAflow Changelog

v2.3.5

count.nf

  • fix hard coded BC length in merge_label.py

v2.3.4

count.nf

  • increasing speed of src/merge_label.py speed for larger MPRAs.

v2.3.3

association.nf

  • Bugfix in src/nf_ori_map_barcodes.py script (see issue #41). Now >= mapq instead of > mapq is used.

v2.3.2

count.nf

  • Bugfix merge_all.py script (see issue #55)

v2.3.1

association.nf

  • Bugfix empty design file (see issue #45)

v2.3

global changes

  • Correcting typos in documentation
  • adding new process label highmem to conf/cluster.config

association_saturationMutagenesis.nf

New association saturation mutagenesis workflow. This workflow is about assocation variant calls with barcodes. Variants are introduced by an error-prone PCR. The workflow takes the sequencing of the region, with barcodes in index read and the reference sequence and maps the reads to the reference, calls variants and associates them with the corresponding barcode. it is a pre-step of saturationMutagenesis.nf.

count.nf

  • using BC threshold input for plot_perInsertCounts_correlation.R instead of hard-coded. Modify process calc_correlations to use the new input theshold.

association.nf

  • Remove "windows" characters in design fasta

v2.2

No workflow changes. Only a few fixes and some restructuring of configs. Using nextflow version 20.01 now!

global changes

  • nextflow version 20.01 is needed because of multiMap() function
  • introducing new config file conf/global.config with global variables like the min. required nextflow version and the actual MPRAflow version.
  • moving cluster config to a sepArate file: conf/cluster.config. Try to adapt the times to the sort and longtime labels. Modify SLURM queue to SLUM not SGE options.
  • improved documentation

saturationMutagenesis.nf

  • Bugfix of default out dir. It was not set to params.outdir = "outs" so it tries to create a folder null. Now in params.outdir
  • removing default params.version and params.nf_required_version. Now in conf/global.config
  • Catching cases when barcode/p-value filtering produces 0 variants
  • Change update depricated fork method. Now works with nextflow 20.01

count.nf

  • removing default params.version, params.nf_required_version and params.outdir. Now in conf/global.config.

association.nf

  • removing default params.version, params.nf_required_version and params.outdir. Now in conf/global.config.

v2.1

Initial MPRAflow version for publication.