report_comment: >
This report has been generated by the nf-core/atacseq
analysis pipeline. For information about how to interpret these results, please see the
documentation.
data_format: 'yaml'
run_modules:
- custom_content
- fastqc
- cutadapt
- samtools
- picard
- preseq
- featureCounts
- deeptools
exclude_modules:
- 'general_stats'
module_order:
- fastqc:
name: 'LIB: FastQC (raw)'
info: 'This section of the report shows FastQC results before adapter trimming for individual libraries.'
path_filters:
- './fastqc/*.zip'
- cutadapt:
name: 'LIB: Cutadapt (trimmed)'
info: 'This section of the report shows the length of trimmed reads by Cutadapt for individual libraries.'
- fastqc:
name: 'LIB: FastQC (trimmed)'
info: 'This section of the report shows FastQC results after adapter trimming for individual libraries.'
path_filters:
- './trimgalore/fastqc/*.zip'
- samtools:
name: 'LIB: SAMTools'
info: 'This section of the report shows SAMTools results for individual libraries.'
path_filters:
- './alignment/library/*'
- samtools:
name: 'MERGED LIB: SAMTools (unfiltered)'
info: 'This section of the report shows SAMTools results after merging libraries and before filtering.'
path_filters:
- './alignment/mergedLibrary/*.mLb.mkD.sorted.bam*'
- preseq:
name: 'MERGED LIB: Preseq (unfiltered)'
info: 'This section of the report shows Preseq results after merging libraries and before filtering.'
- samtools:
name: 'MERGED LIB: SAMTools (filtered)'
info: 'This section of the report shows SAMTools results after merging libraries and after filtering.'
path_filters:
- './alignment/mergedLibrary/*.mLb.clN.sorted.bam*'
- picard:
name: 'MERGED LIB: Picard'
info: 'This section of the report shows picard results after merging libraries and after filtering.'
path_filters:
- './alignment/mergedLibrary/picard_metrics/*'
- deeptools:
name: 'MERGED LIB: deepTools'
anchor: 'mlib_deeptools'
info: 'This section of the report shows QC plots generated by deepTools.'
- featureCounts:
name: 'MERGED LIB: featureCounts'
anchor: 'mlib_featurecounts'
info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
path_filters:
- './macs/mergedLibrary/consensus/*.summary'
- samtools:
name: 'MERGED REP: SAMTools'
info: 'This section of the report shows SAMTools results after merging replicates and filtering.'
path_filters:
- './alignment/mergedReplicate/*'
- picard:
name: 'MERGED REP: Picard'
anchor: 'mrep_picard'
info: 'This section of the report shows picard results after merging libraries and before filtering.'
path_filters:
- './alignment/mergedReplicate/*'
- featureCounts:
name: 'MERGED REP: featureCounts'
anchor: 'mrep_featurecounts'
info: 'This section of the report shows featureCounts results for the number of reads assigned to merged replicate consensus peaks.'
path_filters:
- './macs/mergedReplicate/consensus/*.summary'
report_section_order:
mlib_peak_count:
before: mlib_deeptools
mlib_frip_score:
before: mlib_peak_count
mlib_peak_annotation:
before: mlib_frip_score
mlib_featurecounts:
before: mlib_peak_annotation
mlib_deseq2_pca:
before: mlib_featurecounts
mlib_deseq2_clustering:
before: mlib_deseq2_pca
mrep_peak_count:
before: mrep_picard
mrep_frip_score:
before: mrep_peak_count
mrep_peak_annotation:
before: mrep_frip_score
mrep_featurecounts:
before: mrep_peak_annotation
mrep_deseq2_pca:
before: mrep_featurecounts
mrep_deseq2_clustering:
before: mrep_deseq2_pca
software_versions:
order: -1001
nf-core-atacseq-summary:
order: -1002
custom_plot_config:
picard_insert_size:
cpswitch_c_active: False
smooth_points: 1000
featurecounts:
cpswitch_c_active: False
featurecounts-1:
cpswitch_c_active: False
extra_fn_clean_exts:
- 'fastq.gz'
- '_trimmed'
- '_val'
- 'sorted.bam'
- '.Lb'
- 'mkD'
- 'clN'
- 'mLb'
- 'mRp'
- '_peaks'
# # Customise the module search patterns to speed up execution time
# # - Skip module sub-tools that we are not interested in
# # - Replace file-content searching with filename pattern searching
# # - Don't add anything that is the same as the MultiQC default
# # See https://multiqc.info/docs/#optimise-file-search-patterns for details
sp:
cutadapt:
fn: '*trimming_report.txt'
preseq:
fn: '*.ccurve.txt'
deeptools/plotFingerprintOutRawCounts:
fn: '*plotFingerprint*'
deeptools/plotProfile:
fn: '*plotProfile*'