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nf-core/chipseq: Changelog

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

[2.1.0] - 2024-10-07

Credits

Special thanks to the following people for their contributions to this release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

  • Updated pipeline template to nf-core/tools 2.7.2
  • [#317] - Added metro map
  • [#288] - Bump chromap version 2 and enable all the steps below chromap again when paired-end data is processed.
  • [#311] - Add back --skip_spp parameter which was unintentionally removed from the code.
  • Install available nf-core subworkflows and refactor code accordingly
  • [#318] - Update bowtie2/align module to fix issue when downloading its singularity image.
  • [#320] - Fix samplesheet control column in documentation examples.
  • [#328] - Modify documentation to clarify that is necessary to provide the --read_length when --genome is set and --macs_gsize has not provided.
  • Remove enable_conda param from local modules.
  • Fix the path where chromap index is stored when --save_reference is set.
  • Fix untar of chromap index when using --chromap_index param.
  • nf-core/tools#2286 - Set default container registry outside profile scope.
  • [#343] - Provide replicate information explicitly in samplesheet.
  • Updated pipeline template to nf-core/tools 2.10.
  • [#367] - Get rid of CheckIfExists for params paths.
  • [#370] - Fix stack overflow exceptions in phantompeakqualtools (see here).
  • [#387] - Get rid of the lib folder and rearrange the pipeline accordingly.
  • [#385] - Fix --save_unaligned description in schema.
  • [PR #392] - Adding line numbers to warnings/errors messages in bin/check_samplesheet.py.
  • [#396] - Check that samplesheet samples IDs do only have alphanumeric characters, dots, dashes or underscores.
  • [#378] - Switch from macs2 to macs3.
  • [#347] - Add read group tag to bam files processed by bowtie2.
  • [PR #406] - Update metro map to show macs3 instead of macs2.
  • [#409] - Bulk modules and subworkflows update.
  • [PR #415] - Get rid of oras in modules.
  • [PR #420] - Fix bug on how replicates are set for MACS3 downstream analysis.

Parameters

Old parameter New parameter
--show_hidden_params --validationShowHiddenParams
--version
--hook_url
--multiqc_logo
--multiqc_methods_description
--pipelines_testdata_base_path
--validationFailUnrecognisedParams
--validationLenientMode
--enable_conda

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Old version New version
bowtie2 2.4.4 2.5.2
bwa 0.7.17 0.7.18
chromap 0.2.1 0.2.6
deeptools 3.5.1 3.5.5
fastqc 0.11.9 0.12.1
gffread 0.12.1 0.12.7
macs2 2.2.7.1
macs3 3.0.1
multiqc 1.13 1.23
picard 2.27.4 3.2.0
samtools 1.15.1 1.20
ucsc-bedgraphtobigwig 377 445
umi_tools 1.1.5

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

[2.0.0] - 2022-10-03

Enhancements & fixes

  • Pipeline has been re-implemented in Nextflow DSL2
  • All software containers are now exclusively obtained from Biocontainers
  • Updated pipeline template to nf-core/tools 2.5.1
  • [#128] - Filter files with no peaks to avoid errors in downstream processes
  • [#220] - Fix phantompeakqualtools protection stack overflow error
  • [#233] - Add chromap to the available aligners
  • Bump minimum Nextflow version from 21.04.0 -> 21.10.3
  • Added python3 shebang to appropriate scripts in bin/ directory
  • [#160] - Add bowtie2 and star as available aligners, via the --aligner parameter
  • Add --save_unaligned parameter (only available for bowtie2 and star)
  • Update igenomes.config to fetch whole BWAIndex/version0.6.0/ folder
  • [228] - Update blacklist bed files.
  • nf-core/tools#1415 - Make --outdir a mandatory parameter
  • [282] - Fix genome.fa publication for IGV.
  • [280] - Update macs_gsize in igenomes.config, create a new --read_length parameter and implement the logic to calculate --macs_gsize when the parameter is missing
  • Eliminate if conditions from deseq2_qc and macs2_consensus (local module and use ext.when instead)
  • Remove deseq2 differential binding analysis of consensus peaks.
  • [280 - Filter paired-end files produced by chromap since the resulting BAM files can not be processed downstream.
  • Add bytesize link to readme.

Parameters

Old parameter New parameter
--conda --enable_conda
--skip_diff_analysis --skip_deseq2_qc
--skip_qc
--aligner
--save_unaligned
--read_length
--multiqc_title
--gff
--bowtie2_index
--chromap_index
--star_index
--validate_params
--show_hidden_params
--config_profile_name
--clusterOptions
--single_end
--name
--hostnames

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Old version New version
samtools 1.10 1.15.1
picard 2.23.1 2.27.4
bamtools 2.5.1 2.5.2
pysam 0.15.3 0.19.0
bedtools 2.29.2 2.30.0
ucsc-bedgraphtobigwig 357 377
deeptools 3.4.3 3.5.1
pigz 2.3.4 2.6
preseq 2.0.3 3.1.2
multiqc 1.9 1.13a
r-base 3.6.1 4.0.3
r-ggplot2 3.3.2 3.3.3
bioconductor-deseq2 1.26.0 1.28.0
trim-galore 0.6.5 0.6.7
r-optparse - 1.7.1
chromap - 0.2.1
bowtie2 - 2.4.4
star - 2.6.1d
r-tidyr - -
r-lattice - -
r-xfun - -
bioconductor-vsn - -

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

[1.2.2] - 2021-04-22

  • #206 - Minor patch release to fix Conda environment

Dependencies

  • Update r-base 3.6.2 -> 3.6.3
  • Update r-xfun 0.15 -> 0.20

[1.2.1] - 2020-07-29

  • #171 - Minor patch release to update pipeline schema

[1.2.0] - 2020-07-02

Added

  • #138 - Add social preview image
  • #153 - Add plotHeatmap
  • #159 - expose bwa mem -T parameter
  • nf-core/atacseq#63 - Added multicore support for Trim Galore!
  • nf-core/atacseq#75 - Include gene annotation versions in multiqc report
  • nf-core/atacseq#76 - featureCounts coupled to DESeq2
  • nf-core/atacseq#79 - Parallelize DESeq2
  • nf-core/atacseq#97 - PBC1, PBC2 from pipeline?
  • nf-core/atacseq#107 - Add options to change MACS2 parameters
  • Regenerated screenshots and added collapsible sections for output files in docs/output.md
  • Update template to tools 1.9
  • Replace set with tuple and file() with path() in all processes
  • Capitalise process names
  • Parameters:
    • --bwa_min_score to set minimum alignment score for BWA MEM
    • --macs_fdr to provide FDR threshold for MACS2 peak calling
    • --macs_pvalue to provide p-value threshold for MACS2 peak calling
    • --skip_peak_qc to skip MACS2 peak QC plot generation
    • --skip_peak_annotation to skip annotation of MACS2 and consensus peaks with HOMER
    • --skip_consensus_peaks to skip consensus peak generation
    • --deseq2_vst to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
    • --publish_dir_mode to customise method of publishing results to output directory nf-core/tools#585

Removed

  • --tss_bed parameter

Fixed

  • #118 - Running on with SGE
  • #132 - BigWig Error: sort: cannot create temporary file in '': Read-only file system
  • #154 - computeMatrix.val.mat.gz files not zipped
  • nf-core/atacseq#71 - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
  • nf-core/atacseq#73 - macs_annotatePeaks.mLb.clN.summary.txt file is not created
  • nf-core/atacseq#86 - bug in the plot_homer_annotatepeaks.r script
  • nf-core/atacseq#102 - Incorrect Group ID assigned by featurecounts_deseq2.r
  • nf-core/atacseq#109 - Specify custom gtf but gene bed is not generated from that gtf?
  • Make executables in bin/ compatible with Python 3

Dependencies

  • Add bioconductor-biocparallel 1.20.0
  • Add markdown 3.2.2
  • Add pigz 2.3.4
  • Add pygments 2.6.1
  • Add pymdown-extensions 7.1
  • Add python 3.7.6
  • Add r-reshape2 1.4.4
  • Add r-tidyr 1.1.0
  • Update bedtools 2.27.1 -> 2.29.2
  • Update bioconductor-deseq2 1.20.0 -> 1.26.0
  • Update bioconductor-vsn 3.46.0 -> 3.54.0
  • Update deeptools 3.2.1 -> 3.4.3
  • Update fastqc 0.11.8 -> 0.11.9
  • Update gawk 4.2.1 -> 5.1.0
  • Update homer 4.9.1 -> 4.11
  • Update macs2 2.1.2 -> 2.2.7.1
  • Update multiqc 1.7 -> 1.8
  • Update phantompeakqualtools 1.2 -> 1.2.2
  • Update picard 2.19.0 -> 2.23.1
  • Update pysam 0.15.2 -> 0.15.3
  • Update r-base 3.4.1 -> 3.6.2
  • Update r-ggplot2 3.1.0 -> 3.3.2
  • Update r-lattice 0.20_35 -> 0.20_41
  • Update r-optparse 1.6.0 -> 1.6.6
  • Update r-pheatmap 1.0.10 -> 1.0.12
  • Update r-scales 1.0.0 -> 1.1.1
  • Update r-upsetr 1.3.3 -> 1.4.0
  • Update r-xfun 0.3 -> 0.15
  • Update samtools 1.9 -> 1.10
  • Update subread 1.6.4 -> 2.0.1
  • Update trim-galore 0.5.0 -> 0.6.5
  • Update ucsc-bedgraphtobigwig 377 -> 357

[1.1.0] - 2019-11-05

Added

  • nf-core/atacseq#46 - Missing gene_bed path in igenomes config
  • Update template to tools 1.7
  • Add --trim_nextseq parameter
  • Add CITATIONS.md file
  • Capitalised process names

Fixed

  • Change all parameters from camelCase to snake_case (see Deprecated)
  • nf-core/atacseq#44 - Output directory missing: macs2/consensus/deseq2
  • nf-core/atacseq#45 - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
  • nf-core/atacseq#46 - Stage blacklist file in channel properly
  • nf-core/atacseq#50 - HOMER number of peaks does not correspond to found MACS2 peaks
  • Fixed bug in UpSetR peak intersection plot
  • Increase default resource requirements in base.config
  • Increase process-specific requirements based on user-reported failures

Dependencies

  • Update Nextflow 0.32.0 -> 19.10.0

Deprecated

Deprecated Replacement
--design --input
--singleEnd --single_end
--saveGenomeIndex --save_reference
--skipTrimming --skip_trimming
--saveTrimmed --save_trimmed
--keepDups --keep_dups
--keepMultiMap --keep_multi_map
--saveAlignedIntermediates --save_align_intermeds
--narrowPeak --narrow_peak
--saveMACSPileup --save_macs_pileup
--skipDiffAnalysis --skip_diff_analysis
--skipFastQC --skip_fastqc
--skipPicardMetrics --skip_picard_metrics
--skipPreseq --skip_preseq
--skipPlotProfile --skip_plot_profile
--skipPlotFingerprint --skip_plot_fingerprint
--skipSpp --skip_spp
--skipIGV --skip_igv
--skipMultiQC --skip_multiqc

[1.0.0] - 2019-06-06

Initial release of nf-core/chipseq pipeline.

Added

  • Raw read QC (FastQC)
  • Adapter trimming (Trim Galore!)
  • Map and filter reads (BWA, picard, SAMtools, BEDTools, BAMTools, Pysam)
  • Create library-size normalised bigWig tracks (BEDTools, bedGraphToBigWig)
  • Alignment QC metrics (Preseq, picard)
  • ChIP-seq QC metrics (deepTools, phantompeakqualtools)
  • Call and annotate broad/narrow peaks (MACS2, HOMER)
  • Create consensus set of peaks per antibody (BEDTools)
  • Quantification and differential binding analysis (featureCounts, DESeq2)
  • Collate appropriate files for genome browser visualisation (IGV)
  • Collate and present various QC metrics (MultiQC, R)