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For the first part of the solution, we'll create a modified version of the metrics files, but not in the alignment directory, but in a new for_multiqc directory. 

mkdir -p ~$SCRATCH/playtimebyteclub/multiqc/atacseq02_bowtie/for_multiqc
cd ~$SCRATCH/playtimebyteclub/multiqc/atacseq02_bowtie/for_multiqc
for f in ../bowtie2/*.dupinfo.txt; do
  bn=`basename $f`
  pfx=${bn%%.dupinfo.txt}
  echo "$f - $pfx"
  cat $f | sed 's/[.]sort//g' > ${pfx}.dupmetrics.txt
done

Executing ls -1 ~/playtimeYour $SCRATCH/byteclub/multiqc/atacseq02_bowtie/for_multiqc directory should now show have 2 files:

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• brain_50k_nuclei.fixed.dupmetrics.txt

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• brain_

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• 50k_nuclei.fixed.dupmetrics.txt

The final piece of the puzzle is to tell MultiQC to ignore the original <prefix>.dupinfo.txt files by modifying the multiqc_config.yaml file, adding a fn_ignore_files list entry.

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After making this config file modification, you can now run multiqc again:

cd ~$SCRATCH/playtimebyteclub/multiqc/atacseq02_bowtie; rm -rf mqc_report*; multiqc .

The resulting report will should look like this: ftp://gapdh.icmb.utexas.edu/misc/multiqc/04.mqc_report.fixed_align_info.html

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And again...

cd ~$SCRATCH/playtimebyteclub/multiqc/atacseq02_bowtie; rm -rf mqc_report*; multiqc .

Producing a report like this:    .  ftp://gapdh.icmb.utexas.edu/misc/multiqc/05.mqc_report.changed_section_order.html

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