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TLC for MultiQC
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@drpatelh
drpatelh committed Jul 1, 2020
1 parent 7109c10 commit 67e62fc
Showing 1 changed file with 68 additions and 55 deletions.
123 changes: 68 additions & 55 deletions assets/multiqc_config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,100 +20,98 @@ exclude_modules:

module_order:
- fastqc:
name: 'FastQC (library; raw)'
info: 'This section of the report shows FastQC results before adapter trimming.'
name: 'LIB: FastQC (raw)'
info: 'This section of the report shows FastQC results before adapter trimming for individual libraries.'
path_filters:
- '*_fastqc.zip'
path_filters_exclude:
- '*val*_fastqc.zip'
- '*trimmed_fastqc.zip'
- './fastqc/*.zip'
- cutadapt:
name: 'cutadapt (library; trimmed)'
info: 'This section of the report shows the length of trimmed reads by cutadapt.'
path_filters:
- '*_trimming_report.txt'
name: 'LIB: Cutadapt (trimmed)'
info: 'This section of the report shows the length of trimmed reads by Cutadapt for individual libraries.'
- fastqc:
name: 'FastQC (library; trimmed)'
info: 'This section of the report shows FastQC results after adapter trimming.'
name: 'LIB: FastQC (trimmed)'
info: 'This section of the report shows FastQC results after adapter trimming for individual libraries.'
path_filters:
- '*val*_fastqc.zip'
- '*trimmed_fastqc.zip'
- './trimgalore/fastqc/*.zip'
- samtools:
name: 'SAMTools (library)'
name: 'LIB: SAMTools'
info: 'This section of the report shows SAMTools results for individual libraries.'
path_filters:
- '*.Lb.sorted.bam*'
- './alignment/library/*'
- samtools:
name: 'SAMTools (merged library; unfiltered)'
name: 'MERGED LIB: SAMTools (unfiltered)'
info: 'This section of the report shows SAMTools results after merging libraries and before filtering.'
path_filters:
- '*mLb.mkD.sorted.bam*'
- './alignment/mergedLibrary/*.mLb.mkD.sorted.bam*'
- preseq:
name: 'Preseq (merged library; unfiltered)'
name: 'MERGED LIB: Preseq (unfiltered)'
info: 'This section of the report shows Preseq results after merging libraries and before filtering.'
path_filters:
- '*mLb*'
- samtools:
name: 'SAMTools (merged library; filtered)'
name: 'MERGED LIB: SAMTools (filtered)'
info: 'This section of the report shows SAMTools results after merging libraries and after filtering.'
path_filters:
- '*mLb.clN.sorted.bam*'
- './alignment/mergedLibrary/*.mLb.clN.sorted.bam*'
- picard:
name: 'Picard (merged library; filtered)'
name: 'MERGED LIB: Picard'
info: 'This section of the report shows picard results after merging libraries and after filtering.'
path_filters:
- '*mLb*'
- './alignment/mergedLibrary/picard_metrics/*'
- deeptools:
name: '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:
- '*.plot*'
- './macs/mergedLibrary/consensus/*.summary'
- samtools:
name: 'SAMTools (merged replicate; filtered)'
info: 'This section of the report shows SAMTools results after merging replicates and before filtering.'
name: 'MERGED REP: SAMTools'
info: 'This section of the report shows SAMTools results after merging replicates and filtering.'
path_filters:
- '*mRp.clN*'
- './alignment/mergedReplicate/*'
- picard:
name: 'Picard (merged replicate; filtered)'
name: 'MERGED REP: Picard'
anchor: 'mrep_picard'
info: 'This section of the report shows picard results after merging libraries and before filtering.'
path_filters:
- '*mRp.clN*'
- './alignment/mergedReplicate/*'
- featureCounts:
name: 'featureCounts (merged library)'
info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
path_filters:
- '*mLb.clN.featureCounts*'
- featureCounts:
name: 'featureCounts (merged replicate)'
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:
- '*mRp.clN.featureCounts*'
- './macs/mergedReplicate/consensus/*.summary'

report_section_order:
mlib_peak_count:
order: -1000
mrep_peak_count:
order: -1100
before: mlib_deeptools
mlib_frip_score:
order: -1200
mrep_frip_score:
order: -1300
before: mlib_peak_count
mlib_peak_annotation:
order: -1400
mrep_peak_annotation:
order: -1500
before: mlib_frip_score
mlib_featurecounts:
before: mlib_peak_annotation
mlib_deseq2_pca:
order: -1600
mrep_deseq2_pca:
order: -1700
before: mlib_featurecounts
mlib_deseq2_clustering:
order: -1800
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:
order: -1900
before: mrep_deseq2_pca
software_versions:
order: -2000
order: -1001
nf-core-atacseq-summary:
order: -2100
order: -1002

custom_plot_config:
picard_insert_size:
Expand All @@ -135,3 +133,18 @@ extra_fn_clean_exts:
- '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*'

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