Multiqc output files have changed v1.21

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Hi there,

I’m using multiqc v1.21
I’ve a config file as below. It hasn’t changed.
Earlier I used to have following files:

multiqc_picard_AlignmentSummaryMetrics.txt
multiqc_picard_baseContent.txt
multiqc_picard_insertSize.txt
multiqc_star.txt
multiqc_fastp.txt
multiqc_general_stats.txt
multiqc_sources.txt
multiqc_data.json

Now, the output files are completely different.

fastp-seq-content-n-plot_Read_1_After_filtering.txt
picard_quality_score_distribution.txt
fastp-seq-content-gc-plot_Read_1_After_filtering.txt
picard_quality_by_cycle.txt
picard_insert_size_Percentages.txt
fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
fastp-seq-content-n-plot_Read_1_Before_filtering.txt
fastp-seq-quality-plot_Read_1_After_filtering.txt
fastp-seq-quality-plot_Read_1_Before_filtering.txt
picard_base_distribution_by_cycle__Adenine.txt
fastp_filtered_reads_plot.txt
multiqc_data.json
picard_base_distribution_by_cycle__Undetermined.txt
fastp-seq-quality-plot_Read_2_After_filtering.txt
fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
fastp-seq-content-gc-plot_Read_2_After_filtering.txt
picard_base_distribution_by_cycle__Cytosine.txt
multiqc_citations.txt
picard_insert_size_Counts.txt
star_alignment_plot.txt
multiqc_general_stats.txt
picard_base_distribution_by_cycle__Guanine.txt
picard_base_distribution_by_cycle__Thymine.txt
picard_alignment_summary_Aligned_Reads.txt
picard_alignment_summary_Aligned_Bases.txt
multiqc.log
multiqc_sources.txt
fastp-seq-content-n-plot_Read_2_Before_filtering.txt
fastp-seq-content-n-plot_Read_2_After_filtering.txt
fastp-insert-size-plot.txt
fastp-seq-quality-plot_Read_2_Before_filtering.txt

My config file:

show_analysis_paths: False

sp:
 picard/quality_by_cycle:
  skip: true
 picard/quality_score_distribution:
  skip: true
 picard/insert_size_metrics:
  skip: true
remove_sections:
 - picard_alignment_readlength

I’m unable to understand what happened and how. How do I go back to previous list of files?

2

Hi @complexgenome,

We’ve been doing a lot of refactoring work on MultiQC recently, there have 5 new releases since v1.21 so it’s quite possible that this was a short lived bug that you encountered.

Are you able to test again with v1.23 and see if the exported filenames go back to being what you expect?

If I make a guess at the input files you ran with, I now get outputs that look much more like the ones you pasted from earlier runs:

$ multiqc -f QualityScoreDistributionMetrics InsertSizeMetrics QualityByCycleMetrics

/// MultiQC 🔍 v1.24.dev0

            config | Loading config settings from: /Users/ewels/.multiqc_config.yml
       file_search | Search path: /Users/ewels/GitHub/MultiQC/test-data/data/modules/picard/QualityScoreDistributionMetrics
       file_search | Search path: /Users/ewels/GitHub/MultiQC/test-data/data/modules/picard/InsertSizeMetrics
       file_search | Search path: /Users/ewels/GitHub/MultiQC/test-data/data/modules/picard/QualityByCycleMetrics
         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 21/21
            picard | Found 14 InsertSizeMetrics reports
            picard | Found 4 QualityByCycleMetrics reports
            picard | Found 4 QualityScoreDistributionMetrics reports
     write_results | Data        : /Users/ewels/GitHub/MultiQC/test-data/data/modules/picard/multiqc_data   (overwritten)
     write_results | Report      : /Users/ewels/GitHub/MultiQC/test-data/data/modules/picard/multiqc_report.html   (overwritten)
           multiqc | MultiQC complete

multiqc_data then contains:

multiqc_citations.yaml
multiqc_data.json
multiqc_general_stats.yaml
multiqc_picard_insertSize.yaml
multiqc_picard_quality_by_cycle.yaml
multiqc_picard_quality_score_distribution.yaml
multiqc_sources.yaml
picard_histogram.yaml
picard_histogram_1.yaml
picard_histogram_2.yaml
picard_insert_size_Counts.yaml
picard_insert_size_Percentages.yaml
picard_quality_by_cycle.yaml
picard_quality_score_distribution.yaml

So I’m hoping that this is already resolved.

Phil