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CHANGELOG.md

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nf-core/hicar: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v2.0.0 - [07/13/2023]

  • [#89] - update to nf-core-template-2.9
  • [#90] - remove the output folder setting from config files
  • replace the dots by '_' in the samples group
  • add support for MseI.
  • add TAD, AB compartments, APA analysis (see available tools in usage documentation)
  • add additional methods for interaction caller
  • adjust default resource requirement
  • update the CITAIONS
  • re-arrange the output folder to meet the requirements of multiple analysis tools
  • updated multipe documentations
  • remove the parameter for java resources requirements
  • update annotations from 5k,10k bins to nearest R2 peaks
  • removed local_modules tests
  • add scale factor to atac reads coverage calculation
  • change the circos plot style
  • update reads_summary table to include unmapped/multiple mapped info
  • add the possibility to subsample to balance the input reads
  • add parameter to let user input the 5 end sequence to cutadapt step
  • change the cutadapt error tolerance from 0 to 0.15
  • changes in hipeak caller:
    • add filter condition for lowest count number as 1.
    • change the cutoff value for hipeak type assignment step from 12 to 3.
  • fix multiple bugs:
    • the sorting method for huge bed file;
    • the post count for hipeak when there is empty Interactions;
    • add totalLinks parameter for prepare_circos;
    • the issue if bplapply does not work in differential analysis for hipeak;
    • fix the space issue for enzyme_cut.nf;
    • fix the chromosome style for homer TFEA analysis and annotation by ChIPpeakAnno;
    • fix the duplicated imported modules;
    • fix multiple typos.
    • use local SAMTOOLS_SORT module;

v1.0.0 - [05/03/2022]

  • bump version for release.
  • update the README.md.
  • update Zendo DOI.

v1.0dev - [04/25/2022]

  • add totalLinks parameter for prepare_circos.
  • add filters to chromosome names for hipeak.
  • add parameter anchor_peaks.
  • Update MAPS for new version of VGAM.
  • add parameter publish_dir_mode.
  • add circos plot for MAPS loops.
  • update the old syntax.
  • prepare reads count for hipeak by chromosome.
  • fix the bug for R1 peak calling when the peak is out-of-bound ranges.
  • fix the bug in calling peaks for pospoisson regression
  • simplify the fragment peak calling by call peaks only for fragmentation sites
  • add unit test for local subworkflow
  • change R1 reads name to fragment reads in documentation
  • use hdf5 to improve the IO efficency
  • fix the file path for igv.py
  • improve trackviewer.nf
  • update gunzip module
  • fix a typo in publish_dir of differential analysis.
  • fix the empty output of PCA analysis for multiQC.
  • replace zcat by gunzip -c
  • update documentation of readme
  • fix the wrong estimated genome size for unsupported genome.
  • fix multiple typo.
  • optimize the code for checksums.nf
  • add commit number to source code downloaded from github
  • update igv module
  • update cooler/dump module
  • replace the macs2 module by nf-core/macs2 module
  • keep bedtools version consistent
  • merge rscripts into nf files
  • change ch_juicer_tool and ch_circos_config into value type channel
  • import md5sum from coreutils
  • simplify the shell scripts.
  • fix a bug for .hic file creation if the resolution is greater than coverage region.
  • add documentation for changed source code for MAPS
  • remove paste command from igv.nf
  • fix the bug that annopeaks.r does not creat folder
  • change version number output from txt to yml file.
  • update citation.md
  • change the juicer_tools download on fly
  • resolve questions about installation of R packages
  • remove juicer_tools bin file
  • remove install_packages.r file
  • rename the parepare_circos to circos_prepare
  • update documentation
  • update multiqc_config.yaml file
  • precheck the conditions before doing differential analysis.

change on [11/02/2021]

  • add module to covert pair file to bam for visualization
  • decrease the memory cost for differential analysis
  • add module to create circos plot
  • add module igv
  • add module juicer
  • update QC documentation
  • update the memory cost and add ignore errorStrategy for bedtools sort
  • improve memory cost for modules trackviewer, juicer and prepare_counts
  • handle multiple errors for MAPS
  • update the module to prepare the macs_gsize
  • fix multiple typos in documentation
  • change the filename from design.csv to test_samplesheet.csv
  • change the filename from samplesheet.csv to test_full_samplesheet.csv
  • use nf-core repository URL
  • update the multiqc_config.yaml file format
  • remove the regrexp check for replicate in schema_input.json
  • update output.md
  • update usage.md
  • add container for juicer.nf
  • update nextflow_schema.json