ChIP-Seq data processing workflow
master @ 5655573

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This workflow supports primary processing of ChIP-Seq data from raw reads to genome-wide ChIP signal tracks and ChIP peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.

SEEK ID: https://workflowhub.eu/workflows/1761?version=1

Inputs

ID Name Description Type
sample_id n/a Sample ID used for naming the output files.
  • string
fastq1 n/a List of fastq files containing the first mate of raw reads. Muliple files are provided if multiplexing of the same library has been done on multiple lanes. The reads comming from different fastq files are pooled after alignment. Also see parameter "fastq2".
  • array containing
    • File
fastq2 n/a List of fastq files containing the second mate of raw reads in case of paired end (also see parameter "fastq1"). Important: this list has to be of same length as parameter "fastq1" no matter if paired or single end is used. In case of single end data specify "null" for every entry of fastq1.
  • array containing
    • File
is_paired_end n/a If paired end data is used set to true, else set to false.
  • boolean
adapter1 n/a Adapter sequence for first reads. If not specified (set to "null"), trim_galore will try to autodetect whether ...\n - Illumina universal adapter (AGATCGGAAGAGC)\n - Nextera adapter (CTGTCTCTTATA)\n - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n ... was used.\n You can directly choose one of the above configurations by setting the string to "illumina", "nextera", or "small_rna". Or you specify the adaptor string manually (e.g. "AGATCGGAAGAGC").
  • string?
adapter2 n/a Adapter sequence for second reads (only relevant for paired end data). If it is not specified (set to "null"), trim_galore will try to autodetect whether ...\n - Illumina universal adapter (AGATCGGAAGAGC)\n - Nextera adapter (CTGTCTCTTATA)\n - Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\n ... was used.\n You can directly choose one of the above configurations by setting the string to "illumina", "nextera", or "small_rna". Or you specify the adaptor string manually (e.g. "AGATCGGAAGAGC").
  • string?
genome n/a Path to reference genome in fasta format. Bowtie2 index files (".1.bt2", ".2.bt2", ...) as well as a samtools index (".fai") has to be located in the same directory.\n All of these files can be downloaded for the most common genome builds at https://support.illumina.com/sequencing/sequencing_software/igenome.html. Alternatively, you can use "bowtie2-build" or "samtools index" to create them yourself.
  • File
fragment_size n/a Mean library fragment size, used to reconstruct entire fragments from single end reads. Not relevant in case of paired end data.
  • int?
effective_genome_size n/a The effectively mappable genome size, please see: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
  • long
bin_size n/a Bin size used for generation of coverage tracks. The larger the bin size the smaller are the coverage tracks, however, the less precise is the signal. For single bp resolution set to 1.
  • int
ignoreForNormalization n/a List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. Specify as space-delimited string. Default: "chrX chrY chrM"
  • string?

Steps

ID Name Description
trim_and_map n/a n/a
merge_duprem_filter n/a n/a
chip_qc n/a n/a
generate_coverage_tracks n/a n/a
create_summary_qc_report n/a multiqc summarizes the qc results from fastqc and other tools

Outputs

ID Name Description Type
raw_fastqc_zip n/a n/a
  • array containing
    • array containing
      • File
raw_fastqc_html n/a n/a
  • array containing
    • array containing
      • File
trim_galore_log n/a n/a
  • array containing
    • array containing
      • File
trimmed_fastqc_html n/a n/a
  • array containing
    • array containing
      • File
trimmed_fastqc_zip n/a n/a
  • array containing
    • array containing
      • File
bowtie2_log n/a n/a
  • array containing
    • File
duprem_fastqc_zip n/a n/a
  • array containing
    • File
duprem_fastqc_html n/a n/a
  • array containing
    • File
bam n/a n/a
  • File
picard_markdup_log n/a n/a
  • File
bigwig n/a n/a
  • File
qc_plot_coverage_plot n/a n/a
  • File
qc_plot_coverage_tsv n/a n/a
  • File
qc_plot_fingerprint_plot n/a n/a
  • File?
qc_plot_fingerprint_tsv n/a n/a
  • File?
qc_plot_fingerprint_stderr n/a n/a
  • File
qc_crosscorr_summary n/a n/a
  • File?
qc_crosscorr_plot n/a n/a
  • File?
qc_phantompeakqualtools_stderr n/a n/a
  • File?
multiqc_zip n/a n/a
  • File
multiqc_html n/a n/a
  • File

Version History

master @ 5655573 (earliest) Created 27th Jun 2025 at 15:03 by Pavlo Lutsik

added cwlviewer for the ChIP-Seq workflow


Frozen master 5655573
help Creators and Submitter
Creator
  • Kersten Breuer
Submitter
Tools
Trim Galore
Bowtie 2
SAMtools
MACS
License
Apache License 2.0
Activity

Views: 5   Downloads: 1

Created: 27th Jun 2025 at 15:03

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