modules

bedops_bedmap
The bedmap program is used to retrieve and process signal or other features over regions of interest in BED files
bedops
bedmap
bed
intervals
bedtools_map
Allows one to screen for overlaps between two sets of genomic features. Adapted from https://github.com/nf-core/modules/tree/fff2c3fc7cdcb81a2a37c3263b8ace9b353af407/modules/nf-core/bedtools
bed
vcf
gff
map
bedtools
bedtools_merge
combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. Adapted from https://github.com/nf-core/modules/tree/fff2c3fc7cdcb81a2a37c3263b8ace9b353af407/modules/nf-core/bedtools
bed
merge
bedtools
overlapped bed
bedtools_sort
Sorts a feature file by chromosome and other criteria. Adapted from https://github.com/nf-core/modules/tree/fff2c3fc7cdcb81a2a37c3263b8ace9b353af407/modules/nf-core/bedtools
bed
sort
bedtools
chromosome
bwa_index
Create BWA index for reference genome. Adapted from the nf-core bwa index module.
index
fasta
genome
reference
bwa_mem
Performs fastq alignment to a fasta reference using BWA. Adapted from the nf-core bwa-mem module.
mem
bwa
alignment
map
fastq
bam
sam
cat_cat
A module for concatenation of gzipped or uncompressed files. Adapted from the nf-core cat module https://github.com/nf-core/modules/tree/9326d73af3fbe2ee90d9ce0a737461a727c5118e/modules/nf-core/cat
concatenate
gzip
cat
cat_fastq
Concatenates fastq files. Adapted from the nf-core cat module https://github.com/nf-core/modules/tree/9326d73af3fbe2ee90d9ce0a737461a727c5118e/modules/nf-core/cat
cat
fastq
concatenate
convert_sicer

Convert SICER output to BED and broadPeak format

sicer
peaks
chipseq
bed
broadPeak
custom_bam2fastq

The module converts a BAM file to FASTQ format. It uses samtools bam2fq if reads are single end, or picard SamToFastq if reads are paired.

bam2fq
samtools
fastq
picard
custom_bed2saf

The module converts a BED file to SAF (simplified annotation format)

bed
saf
annotation
custom_combinepeakcounts
combine counts into consensus peaks
chipseq
peaks
consensus
custom_consensuspeaks

Find consensus peaks from two or more peak files. The consensus_peaks subworkflow is a re-implementation of this module; new pipelines should use the subworkflow instead.

peaks
chipseq
normalization
consensus
custom_countfastq

Count reads in a fastq file

fastq
biopython
python
custom_formatmergedbed

Reformat consensus peaks from bedtools merge. Used in the consensus_peaks subworkflow.

chipseq
peaks
consensus
bedtools
custom_normalizepeaks
normalize p-values and q-values of consensus peaks with the method from Corces et al. (https://doi.org/10.1126/science.aav1898)
chipseq
peaks
consensus
normalization
cutadapt
Perform adapter/quality trimming on sequencing reads. Adapted from the nf-core cutadapt module.
trimming
adapter trimming
adapters
quality trimming
khmer_uniquekmers
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more. Adapted from nf-core/modules khmer/uniquekhmers.
khmer
k-mer
effective genome size
picard_samtofastq
Converts a BAM or SAM file to fastq. Adapted from the nf-core gatk4 samtofastq module.
fastq
bam
sam
samtools_filteraligned
Filter out aligned reads from a BAM file.
bam
filter
samtools
samtools_flagstat
Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
stats
mapping
counts
bam
sam
cram
samtools_sort
Sort a SAM/BAM/CRAM file. Adapted from the nf-core samtools sort module.
sort
bam
sam
cram
sort_bed
sort a bed file by chromosome then by start position
sort
bed
genomics
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