report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/atacseq/2.1.0" target="_blank">nf-core/atacseq</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/atacseq/2.1.0/output" target="_blank">documentation</a>.

data_format: "yaml"

export_plots: true

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/merged_library/unfiltered/*.mLb.mkD.sorted*"
  - picard:
      name: "MERGED LIB: Picard (unfiltered)"
      info: "This section of the report shows picard results after merging libraries and before filtering."
      path_filters:
        - "./alignment/merged_library/unfiltered/picard_metrics/*"
  - 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/merged_library/filtered/*.mLb.clN.sorted*"
  - picard:
      name: "MERGED LIB: Picard (filtered)"
      info: "This section of the report shows picard results after merging libraries and after filtering."
      path_filters:
        - "./alignment/merged_library/filtered/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:
        - "./macs2/merged_library/featurecounts/*.summary"
  - samtools:
      name: "MERGED REP: SAMTools"
      info: "This section of the report shows SAMTools results after merging replicates and filtering."
      path_filters:
        - "./alignment/merged_replicate/*"
  - 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/merged_replicate/picard_metrics/*"
  - 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:
        - "./macs2/merged_replicate/featurecounts/*.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_1:
    before: mlib_featurecounts
  mlib_deseq2_clustering_1:
    before: mlib_deseq2_pca_1
  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_1:
    before: mrep_featurecounts
  mrep_deseq2_clustering_1:
    before: mrep_deseq2_pca_1
  "nf-core-atacseq-methods-description":
    order: -1000
  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"
  - ".FRiP"
  - ".peak"
  - "lc_extrap"

# # 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: "*.lc_extrap.txt"
  deeptools/plotFingerprintOutRawCounts:
    fn: "*plotFingerprint*"
  deeptools/plotProfile:
    fn: "*plotProfile*"
