multiqc_config.yml

report_comment: >
      For information about how to interpret these results, please see the
      <a href="https://github.com/nf-core/atacseq/blob/master/docs/output.md" target="_blank">documentation</a>.
data_format: "yaml"
module_order:
      - fastqc:
              name: "FastQC (raw)"
              info: "This section of the report shows FastQC results before adapter trimming for individual libraries."
              path_filters: "*_FASTQC/*.zip"
      - cutadapt:
              name: "Cutadapt (trimmed)"
              info: "This section of the report shows the length of trimmed reads by Cutadapt for individual libraries."
      - fastqc:
              name: "FastQC (trimmed)"
              info: "This section of the report shows FastQC results after adapter trimming for individual libraries."
              path_filters: "*_TRIM/*.zip"
      - bowtie2:
              name: "Bowtie2 Alignement (Target Genome)"
              info: "This section of the report shows the alignment after adapter trimming for individual libraries."
              path_filters_exclude: "*_spikein.bowtie2.log"
      - picard:
              name: "Picard Mark Duplicates (Target Genome)"
              info: "This section of the report shows picard mark duplicate results after adapter trimming"
      - bowtie2:
              name: "Bowtie2 Alignement (Spikein Genome)"
              info: "This section of the report shows the alignment after adapter trimming for individual libraries."
              path_filters: "*_spikein.bowtie2.log"
      - samtools
      - deeptools