ChIP-seq peak-calling, QC and differential analysis pipeline.
phantompeakqualtools
protection stack overflow errorchromap
to the available aligners21.04.0
-> 21.10.3
python3
shebang to appropriate scripts in bin/
directorybowtie2
and star
as available aligners, via the --aligner
parameter--save_unaligned
parameter (only available for bowtie2
and star
)igenomes.config
to fetch whole BWAIndex/version0.6.0/
folder--outdir
a mandatory parametergenome.fa
publication for IGV.macs_gsize
in igenomes.config
, create a new --read_length
parameter and implement the logic to calculate --macs_gsize
when the parameter is missingif
conditions from deseq2_qc
and macs2_consensus
(local module and use ext.when
instead)deseq2
differential binding analysis of consensus peaks.chromap
since the resulting BAM
files can not be processed downstream.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.
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.
Dependencies
3.6.2
-> 3.6.3
0.15
-> 0.20
Added
docs/output.md
1.9
set
with tuple
and file()
with path()
in all processes--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
parameterFixed
bin/
compatible with Python 3Dependencies
1.20.0
3.2.2
2.3.4
2.6.1
7.1
3.7.6
1.4.4
1.1.0
2.27.1
-> 2.29.2
1.20.0
-> 1.26.0
3.46.0
-> 3.54.0
3.2.1
-> 3.4.3
0.11.8
-> 0.11.9
4.2.1
-> 5.1.0
4.9.1
-> 4.11
2.1.2
-> 2.2.7.1
1.7
-> 1.8
1.2
-> 1.2.2
2.19.0
-> 2.23.1
0.15.2
-> 0.15.3
3.4.1
-> 3.6.2
3.1.0
-> 3.3.2
0.20_35
-> 0.20_41
1.6.0
-> 1.6.6
1.0.10
-> 1.0.12
1.0.0
-> 1.1.1
1.3.3
-> 1.4.0
0.3
-> 0.15
1.9
-> 1.10
1.6.4
-> 2.0.1
0.5.0
-> 0.6.5
377
-> 357
Added
1.7
--trim_nextseq
parameterCITATIONS.md
fileFixed
camelCase
to snake_case
(see Deprecated)
base.config
Dependencies
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 |
Initial release of nf-core/chipseq pipeline.
Added