nf-core/chipseq v2.0 - Platinum Goldfinch

[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.