---
# System prepended metadata

title: taxprofiler nf-test-snapshot
tags: [taxprofiler]

---

# Taxprofiler nf-test snapshot

## General approach to nf-test

Order of priority (most ideal to least ideal)

1. Stable contents: use md5sums [DEFAULT FOR NF-TEST]
2. Partial unstable contents: validate sections of content
    - plain-text: check for strings in plain text files
    - plain-text: check for number of lines
    - plain-text: check for length of lines
    - binary-files: file size for binary files (unless there is a specific plugin for that format)
    - etc...
4. Fully unstable contents: check for file existance only (i.e., file name)
5. Unstable name: ignore 

Order of operations in order of preference

```mermaid
---
title: nf-core preferences for file checking methods with nf-test
---

graph TD

subgraph 1st class checks: all files
  md5sums("🥇 md5sums")
end 

subgraph 2nd class: plain text files
  md5sums --partly variable contents?--> string_contents("🥈 string contents")
  md5sums --partly variable contents?--> number_lines("🥈 number of lines")
end

subgraph 2nd class: binary files
  md5sums --partly variable contents?--> plugin("🥈 plug in")
  md5sums --partly variable contents?--> file_size("🥈 file size")
end

subgraph 3rd class: all files
  string_contents --totally variable contents?--> file_existence("🥉 just existence of file")
  number_lines--totally variable contents?-->file_existence
  file_size --totally variable contents?--> file_existence
  plugin --totally variable contents?-->file_existence
end

subgraph prison: all file
  file_existence --name & content unstable?--> ignore('😭 exclude')
end
```

## To generate

1. Specify at the top of your test file a variable caled `stable_name_all` that will emit every single output file in `--outdir`
    - You may need to update this variable to ignore files with unstable names (e.g. when the date is in the name)
    - You do not need to have one called `stable_path`  
    - This variable must NOT include `.nftignore`
3. For each output folder, specify a variable called `stable_contents` that specifies the path to each `--outdir` subdirectory inside the `getAllFilesFromDir()` function
    - This function should specify `ignoreFile: .nftignore`
5. Make an `match()`-named snapshot assertion for each output folder, that includes `stable_contents`
6. Run nf-test to generate a snapshot with all md5sums for all files
7. Run nf-test again to identify variable files
8. For all files that were unstable in between runs, add paths to `.nftignore`
    - You can use glob patterns for this if you see a pattern in the unstable files
    - This file should tell nf-test to exclude the paths from `stable_contents`, but keep in `stable_name_all`
    - SOFIA PERSONAL NOTE: 
        - Add `ignoreFile` instead and remove the `stable_name` lines.
        - https://nvnieuwk.github.io/nft-bam/latest/usage/#bam-sam-cram-function to read bam files
        - Define it under nf-test config
9. For each unstable file, make new assertions for within the `snapshot()` of each directory, after the `stable_contents` varaible, to check parts of the file contents (e.g., strings, number of  lines etc.)
    - You can use glob patterns if consistent
11. Re-run nf-test with `--update-snapshot` to make the final snapshot

## File Treee

`-profile test`

```
$ cat out.txt 
[561M]  .
├── [7.9K]  bbduk
│   ├── [1011]  2612_ERR5766176_B.bbduk.log
│   ├── [1003]  2612_ERR5766176.bbduk.log
│   ├── [1009]  2612_ERR5766180.bbduk.log
│   └── [1001]  2613_ERR5766181.bbduk.log
├── [8.8K]  bowtie2
│   └── [4.8K]  align
│       ├── [ 202]  2612_ERR5766176_B.bowtie2.log
│       ├── [ 202]  2612_ERR5766176.bowtie2.log
│       ├── [ 204]  2612_ERR5766180.bowtie2.log
│       └── [ 202]  2613_ERR5766181.bowtie2.log
├── [ 16K]  bracken
│   ├── [ 301]  bracken_db1_combined_reports.txt
│   └── [ 11K]  db1
│       ├── [2.4K]  2611_db1.bracken.kraken2.report_bracken.txt
│       ├── [ 183]  2611_db1.bracken.tsv
│       ├── [2.5K]  2612_db1.bracken.kraken2.report_bracken.txt
│       ├── [ 185]  2612_db1.bracken.tsv
│       ├── [2.0K]  2613_db1.bracken.kraken2.report_bracken.txt
│       └── [ 135]  2613_db1.bracken.tsv
├── [218M]  centrifuge
│   ├── [3.9K]  centrifuge_db3_combined_reports.txt
│   └── [218M]  db3
│       ├── [547K]  2612_db3.centrifuge.mapped.fastq.gz
│       ├── [ 175]  2612_db3.centrifuge.report.txt
│       ├── [ 77M]  2612_db3.centrifuge.results.txt
│       ├── [3.0K]  2612_db3.centrifuge.txt
│       ├── [ 96M]  2612_db3.centrifuge.unmapped.fastq.gz
│       ├── [ 14K]  2613_db3.centrifuge.mapped.fastq.gz
│       ├── [ 171]  2613_db3.centrifuge.report.txt
│       ├── [ 18M]  2613_db3.centrifuge.results.txt
│       ├── [3.0K]  2613_db3.centrifuge.txt
│       └── [ 26M]  2613_db3.centrifuge.unmapped.fastq.gz
├── [3.3M]  diamond
│   ├── [1.5M]  db1
│   │   ├── [ 11K]  2611_db1.diamond.log
│   │   ├── [188K]  2611_db1.diamond.tsv
│   │   ├── [ 11K]  2612_db1.diamond.log
│   │   ├── [967K]  2612_db1.diamond.tsv
│   │   ├── [ 11K]  2613_db1.diamond.log
│   │   └── [322K]  2613_db1.diamond.tsv
│   ├── [313K]  db2
│   │   ├── [ 11K]  2614_db2.diamond.log
│   │   ├── [222K]  2614_db2.diamond.tsv
│   │   ├── [ 11K]  ERR3201952_db2.diamond.log
│   │   └── [ 66K]  ERR3201952_db2.diamond.tsv
│   └── [1.5M]  db3
│       ├── [ 11K]  2611_db3.diamond.log
│       ├── [188K]  2611_db3.diamond.tsv
│       ├── [ 11K]  2612_db3.diamond.log
│       ├── [967K]  2612_db3.diamond.tsv
│       ├── [ 11K]  2613_db3.diamond.log
│       ├── [322K]  2613_db3.diamond.tsv
│       ├── [ 11K]  2614_db3.diamond.log
│       ├── [ 14K]  2614_db3.diamond.tsv
│       ├── [ 11K]  ERR3201952_db3.diamond.log
│       └── [6.0K]  ERR3201952_db3.diamond.tsv
├── [1.7M]  fastp
│   ├── [372K]  2612_ERR5766176_B.fastp.html
│   ├── [108K]  2612_ERR5766176_B.fastp.json
│   ├── [1.5K]  2612_ERR5766176_B.fastp.log
│   ├── [372K]  2612_ERR5766176.fastp.html
│   ├── [108K]  2612_ERR5766176.fastp.json
│   ├── [1.5K]  2612_ERR5766176.fastp.log
│   ├── [236K]  2612_ERR5766180.fastp.html
│   ├── [ 64K]  2612_ERR5766180.fastp.json
│   ├── [ 958]  2612_ERR5766180.fastp.log
│   ├── [372K]  2613_ERR5766181.fastp.html
│   ├── [108K]  2613_ERR5766181.fastp.json
│   └── [1.5K]  2613_ERR5766181.fastp.log
├── [ 13M]  fastqc
│   ├── [5.3M]  processed
│   │   ├── [674K]  2612_ERR5766176_B_processed_fastqc.html
│   │   ├── [422K]  2612_ERR5766176_B_processed_fastqc.zip
│   │   ├── [674K]  2612_ERR5766176_processed_fastqc.html
│   │   ├── [422K]  2612_ERR5766176_processed_fastqc.zip
│   │   ├── [607K]  2612_ERR5766180_processed_fastqc.html
│   │   ├── [420K]  2612_ERR5766180_processed_fastqc.zip
│   │   ├── [669K]  2613_ERR5766181_processed_fastqc.html
│   │   ├── [429K]  2613_ERR5766181_processed_fastqc.zip
│   │   ├── [678K]  ERR3201952_ERR3201952_processed_fastqc.html
│   │   └── [393K]  ERR3201952_ERR3201952_processed_fastqc.zip
│   └── [7.8M]  raw
│       ├── [575K]  2612_ERR5766176_B_raw_1_fastqc.html
│       ├── [405K]  2612_ERR5766176_B_raw_1_fastqc.zip
│       ├── [582K]  2612_ERR5766176_B_raw_2_fastqc.html
│       ├── [417K]  2612_ERR5766176_B_raw_2_fastqc.zip
│       ├── [575K]  2612_ERR5766176_raw_1_fastqc.html
│       ├── [405K]  2612_ERR5766176_raw_1_fastqc.zip
│       ├── [582K]  2612_ERR5766176_raw_2_fastqc.html
│       ├── [417K]  2612_ERR5766176_raw_2_fastqc.zip
│       ├── [600K]  2612_ERR5766180_raw_fastqc.html
│       ├── [450K]  2612_ERR5766180_raw_fastqc.zip
│       ├── [577K]  2613_ERR5766181_raw_1_fastqc.html
│       ├── [418K]  2613_ERR5766181_raw_1_fastqc.zip
│       ├── [590K]  2613_ERR5766181_raw_2_fastqc.html
│       ├── [428K]  2613_ERR5766181_raw_2_fastqc.zip
│       ├── [619K]  ERR3201952_ERR3201952_raw_fastqc.html
│       └── [372K]  ERR3201952_ERR3201952_raw_fastqc.zip
├── [ 15K]  ganon
│   ├── [ 11K]  db1
│   │   ├── [ 863]  2611_db1.ganon.log
│   │   ├── [ 684]  2611_db1.ganon.rep
│   │   ├── [  84]  2611_db1.ganon_report.tre
│   │   ├── [ 565]  2611_db1.ganon.tre
│   │   ├── [ 980]  2612_db1.ganon.log
│   │   ├── [ 910]  2612_db1.ganon.rep
│   │   ├── [  91]  2612_db1.ganon_report.tre
│   │   ├── [ 614]  2612_db1.ganon.tre
│   │   ├── [ 972]  2613_db1.ganon.log
│   │   ├── [ 876]  2613_db1.ganon.rep
│   │   ├── [  88]  2613_db1.ganon_report.tre
│   │   └── [ 597]  2613_db1.ganon.tre
│   └── [  98]  ganon_db1_combined_reports.txt
├── [127M]  kaiju
│   ├── [ 63M]  db5
│   │   ├── [ 213]  2611_db5.kaijutable.txt
│   │   ├── [ 16M]  2611_db5.kaiju.tsv
│   │   ├── [ 214]  2612_db5.kaijutable.txt
│   │   ├── [ 38M]  2612_db5.kaiju.tsv
│   │   ├── [ 213]  2613_db5.kaijutable.txt
│   │   └── [9.0M]  2613_db5.kaiju.tsv
│   ├── [292K]  db6
│   │   ├── [ 212]  2614_db6.kaijutable.txt
│   │   ├── [222K]  2614_db6.kaiju.tsv
│   │   ├── [ 229]  ERR3201952_db6.kaijutable.txt
│   │   └── [ 66K]  ERR3201952_db6.kaiju.tsv
│   ├── [ 63M]  db7
│   │   ├── [ 213]  2611_db7.kaijutable.txt
│   │   ├── [ 16M]  2611_db7.kaiju.tsv
│   │   ├── [ 214]  2612_db7.kaijutable.txt
│   │   ├── [ 38M]  2612_db7.kaiju.tsv
│   │   ├── [ 213]  2613_db7.kaijutable.txt
│   │   ├── [9.0M]  2613_db7.kaiju.tsv
│   │   ├── [ 212]  2614_db7.kaijutable.txt
│   │   ├── [222K]  2614_db7.kaiju.tsv
│   │   ├── [ 229]  ERR3201952_db7.kaijutable.txt
│   │   └── [ 66K]  ERR3201952_db7.kaiju.tsv
│   ├── [ 562]  kaiju_db5_combined_reports.txt
│   ├── [ 402]  kaiju_db6_combined_reports.txt
│   └── [ 925]  kaiju_db7_combined_reports.txt
├── [9.1K]  kmcp
│   └── [5.1K]  db1
│       ├── [ 281]  2611_db1.kmcp.profile
│       ├── [ 428]  2612_db1.kmcp.profile
│       └── [ 422]  2613_db1.kmcp.profile
├── [146M]  kraken2
│   ├── [4.0K]  db1
│   ├── [146M]  db2
│   │   ├── [4.3K]  2611_db2.kraken2.classified.fastq.gz
│   │   ├── [2.6K]  2611_db2.kraken2.kraken2.report.txt
│   │   ├── [ 24M]  2611_db2.kraken2.unclassified.fastq.gz
│   │   ├── [ 20K]  2612_db2.kraken2.classified.fastq.gz
│   │   ├── [2.6K]  2612_db2.kraken2.kraken2.report.txt
│   │   ├── [ 96M]  2612_db2.kraken2.unclassified.fastq.gz
│   │   ├── [4.5K]  2613_db2.kraken2.classified.fastq.gz
│   │   ├── [2.6K]  2613_db2.kraken2.kraken2.report.txt
│   │   └── [ 26M]  2613_db2.kraken2.unclassified.fastq.gz
│   ├── [3.6K]  kraken2_db1-bracken_combined_reports.txt
│   └── [3.6K]  kraken2_db2_combined_reports.txt
├── [1.3M]  krona
│   ├── [223K]  centrifuge_db3.html
│   ├── [221K]  kaiju_db5.html
│   ├── [221K]  kaiju_db6.html
│   ├── [221K]  kaiju_db7.html
│   ├── [224K]  kraken2-bracken_db1.html
│   └── [224K]  kraken2_db2.html
├── [790K]  metaphlan
│   ├── [7.5K]  metaphlan3
│   │   ├── [ 284]  2611_metaphlan3.metaphlan.biom
│   │   ├── [  37]  2611_metaphlan3.metaphlan.bowtie2out.txt
│   │   ├── [ 518]  2611_metaphlan3.metaphlan_profile.txt
│   │   ├── [ 363]  2611_metaphlan3.metaphlan.sam
│   │   ├── [ 284]  2612_metaphlan3.metaphlan.biom
│   │   ├── [  49]  2612_metaphlan3.metaphlan.bowtie2out.txt
│   │   ├── [ 509]  2612_metaphlan3.metaphlan_profile.txt
│   │   ├── [ 360]  2612_metaphlan3.metaphlan.sam
│   │   ├── [ 284]  2613_metaphlan3.metaphlan.biom
│   │   ├── [  50]  2613_metaphlan3.metaphlan.bowtie2out.txt
│   │   ├── [ 522]  2613_metaphlan3.metaphlan_profile.txt
│   │   └── [ 360]  2613_metaphlan3.metaphlan.sam
│   ├── [778K]  metaphlan4
│   │   ├── [ 284]  2611_metaphlan4.metaphlan.biom
│   │   ├── [ 724]  2611_metaphlan4.metaphlan.bowtie2out.txt
│   │   ├── [ 513]  2611_metaphlan4.metaphlan_profile.txt
│   │   ├── [158K]  2611_metaphlan4.metaphlan.sam
│   │   ├── [ 904]  2612_metaphlan4.metaphlan.biom
│   │   ├── [ 28K]  2612_metaphlan4.metaphlan.bowtie2out.txt
│   │   ├── [1.3K]  2612_metaphlan4.metaphlan_profile.txt
│   │   ├── [370K]  2612_metaphlan4.metaphlan.sam
│   │   ├── [ 904]  2613_metaphlan4.metaphlan.biom
│   │   ├── [6.7K]  2613_metaphlan4.metaphlan.bowtie2out.txt
│   │   ├── [1.3K]  2613_metaphlan4.metaphlan_profile.txt
│   │   └── [206K]  2613_metaphlan4.metaphlan.sam
│   ├── [ 147]  metaphlan_metaphlan3_combined_reports.txt
│   └── [ 879]  metaphlan_metaphlan4_combined_reports.txt
├── [ 33M]  multiqc
│   ├── [ 12M]  multiqc_data
│   │   ├── [ 190]  bbduk-filtered-barplot_Bases.txt
│   │   ├── [ 175]  bbduk-filtered-barplot_Reads.txt
│   │   ├── [ 724]  bbduk.txt
│   │   ├── [ 192]  bowtie2_se_plot.txt
│   │   ├── [ 154]  bracken-top-n-plot_Class.txt
│   │   ├── [ 126]  bracken-top-n-plot_Domain.txt
│   │   ├── [ 158]  bracken-top-n-plot_Family.txt
│   │   ├── [ 148]  bracken-top-n-plot_Genus.txt
│   │   ├── [ 143]  bracken-top-n-plot_Kingdom.txt
│   │   ├── [ 156]  bracken-top-n-plot_Order.txt
│   │   ├── [ 149]  bracken-top-n-plot_Phylum.txt
│   │   ├── [ 167]  bracken-top-n-plot_Species.txt
│   │   ├── [ 122]  bracken-top-n-plot_Unclassified.txt
│   │   ├── [ 126]  centrifuge-top-n-plot_Class.txt
│   │   ├── [ 102]  centrifuge-top-n-plot_Domain.txt
│   │   ├── [ 126]  centrifuge-top-n-plot_Family.txt
│   │   ├── [ 117]  centrifuge-top-n-plot_Genus.txt
│   │   ├── [ 125]  centrifuge-top-n-plot_Kingdom.txt
│   │   ├── [ 122]  centrifuge-top-n-plot_Order.txt
│   │   ├── [ 125]  centrifuge-top-n-plot_Phylum.txt
│   │   ├── [ 134]  centrifuge-top-n-plot_Species.txt
│   │   ├── [  98]  centrifuge-top-n-plot_Unclassified.txt
│   │   ├── [ 170]  diamond.txt
│   │   ├── [ 282]  fastp_filtered_reads_plot.txt
│   │   ├── [ 20K]  fastp-insert-size-plot.txt
│   │   ├── [ 15K]  fastp-seq-content-gc-plot_Merged_and_filtered.txt
│   │   ├── [2.9K]  fastp-seq-content-gc-plot_Read_1_After_filtering.txt
│   │   ├── [ 11K]  fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
│   │   ├── [8.1K]  fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
│   │   ├── [ 13K]  fastp-seq-content-n-plot_Merged_and_filtered.txt
│   │   ├── [2.7K]  fastp-seq-content-n-plot_Read_1_After_filtering.txt
│   │   ├── [ 12K]  fastp-seq-content-n-plot_Read_1_Before_filtering.txt
│   │   ├── [9.2K]  fastp-seq-content-n-plot_Read_2_Before_filtering.txt
│   │   ├── [ 12K]  fastp-seq-quality-plot_Merged_and_filtered.txt
│   │   ├── [2.6K]  fastp-seq-quality-plot_Read_1_After_filtering.txt
│   │   ├── [8.9K]  fastp-seq-quality-plot_Read_1_Before_filtering.txt
│   │   ├── [6.8K]  fastp-seq-quality-plot_Read_2_Before_filtering.txt
│   │   ├── [ 11K]  fastqc-1_adapter_content_plot.txt
│   │   ├── [ 237]  fastqc-1_overrepresented_sequences_plot.txt
│   │   ├── [6.5K]  fastqc-1_per_base_n_content_plot.txt
│   │   ├── [7.2K]  fastqc-1_per_base_sequence_quality_plot.txt
│   │   ├── [ 10K]  fastqc-1_per_sequence_gc_content_plot_Counts.txt
│   │   ├── [ 13K]  fastqc-1_per_sequence_gc_content_plot_Percentages.txt
│   │   ├── [1.3K]  fastqc-1_per_sequence_quality_scores_plot.txt
│   │   ├── [ 200]  fastqc-1_sequence_counts_plot.txt
│   │   ├── [1.7K]  fastqc-1_sequence_duplication_levels_plot.txt
│   │   ├── [ 509]  fastqc-1-status-check-heatmap.txt
│   │   ├── [ 510]  fastqc-1_top_overrepresented_sequences_table.txt
│   │   ├── [ 16K]  fastqc_adapter_content_plot.txt
│   │   ├── [ 355]  fastqc_overrepresented_sequences_plot.txt
│   │   ├── [8.0K]  fastqc_per_base_n_content_plot.txt
│   │   ├── [7.8K]  fastqc_per_base_sequence_quality_plot.txt
│   │   ├── [ 12K]  fastqc_per_sequence_gc_content_plot_Counts.txt
│   │   ├── [ 20K]  fastqc_per_sequence_gc_content_plot_Percentages.txt
│   │   ├── [3.0K]  fastqc_per_sequence_quality_scores_plot.txt
│   │   ├── [ 343]  fastqc_sequence_counts_plot.txt
│   │   ├── [2.8K]  fastqc_sequence_duplication_levels_plot.txt
│   │   ├── [2.0K]  fastqc_sequence_length_distribution_plot.txt
│   │   ├── [ 687]  fastqc-status-check-heatmap.txt
│   │   ├── [ 512]  fastqc_top_overrepresented_sequences_table.txt
│   │   ├── [ 268]  kaiju-topfive-plot.txt
│   │   ├── [ 130]  kraken-top-n-plot_Class.txt
│   │   ├── [ 102]  kraken-top-n-plot_Domain.txt
│   │   ├── [ 134]  kraken-top-n-plot_Family.txt
│   │   ├── [ 124]  kraken-top-n-plot_Genus.txt
│   │   ├── [ 119]  kraken-top-n-plot_Kingdom.txt
│   │   ├── [ 132]  kraken-top-n-plot_Order.txt
│   │   ├── [ 125]  kraken-top-n-plot_Phylum.txt
│   │   ├── [ 143]  kraken-top-n-plot_Species.txt
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│   │   ├── [ 286]  metaphlan-top-n-plot_Kingdom.txt
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│   │   ├── [ 288]  metaphlan-top-n-plot_Phylum.txt
│   │   ├── [ 297]  metaphlan-top-n-plot_Species.txt
│   │   ├── [ 307]  multiqc_bowtie2.txt
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│   │   ├── [397K]  multiqc_fastp.txt
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│   │   ├── [ 335]  multiqc_kaiju_species.txt
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│   │   ├── [1.2K]  multiqc_metaphlan.txt
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│   │   ├── [ 133]  nanoq_plot_length_plot.txt
│   │   ├── [ 101]  nanoq_plot_quality_plot.txt
│   │   ├── [ 212]  nanoq_table.txt
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│   │   ├── [ 695]  nonpareil-table.txt
│   │   ├── [  58]  porechop-endtrim-barplot.txt
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│   │   ├── [ 392]  porechop_porechop_abi.txt
│   │   ├── [  62]  porechop-starttrim-barplot.txt
│   │   ├── [ 214]  samtools_alignment_plot.txt
│   │   └── [ 699]  samtools-stats-dp.txt
│   ├── [ 14M]  multiqc_plots
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│   │   │   ├── [ 12K]  bbduk-filtered-barplot_Bases-cnt.pdf
│   │   │   ├── [ 12K]  bbduk-filtered-barplot_Bases-pct.pdf
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│   │   │   ├── [ 13K]  bracken-top-n-plot_Phylum-cnt.pdf
│   │   │   ├── [ 13K]  bracken-top-n-plot_Phylum-pct.pdf
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│   │   │   ├── [ 12K]  bracken-top-n-plot_Unclassified-cnt.pdf
│   │   │   ├── [ 12K]  bracken-top-n-plot_Unclassified-pct.pdf
│   │   │   ├── [ 11K]  centrifuge-top-n-plot_Class-cnt.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Class-pct.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Domain-cnt.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Domain-pct.pdf
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│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Genus-cnt.pdf
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│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Kingdom-cnt.pdf
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│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Order-pct.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Phylum-cnt.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Phylum-pct.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Species-cnt.pdf
│   │   │   ├── [ 12K]  centrifuge-top-n-plot_Species-pct.pdf
│   │   │   ├── [ 13K]  fastp_filtered_reads_plot-cnt.pdf
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│   │   │   ├── [ 15K]  fastp-seq-content-gc-plot_Merged_and_filtered.pdf
│   │   │   ├── [ 12K]  fastp-seq-content-gc-plot_Read_1_After_filtering.pdf
│   │   │   ├── [ 14K]  fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf
│   │   │   ├── [ 13K]  fastp-seq-content-gc-plot_Read_2_Before_filtering.pdf
│   │   │   ├── [ 12K]  fastp-seq-content-n-plot_Merged_and_filtered.pdf
│   │   │   ├── [ 12K]  fastp-seq-content-n-plot_Read_1_After_filtering.pdf
│   │   │   ├── [ 13K]  fastp-seq-content-n-plot_Read_1_Before_filtering.pdf
│   │   │   ├── [ 13K]  fastp-seq-content-n-plot_Read_2_Before_filtering.pdf
│   │   │   ├── [ 13K]  fastp-seq-quality-plot_Merged_and_filtered.pdf
│   │   │   ├── [ 13K]  fastp-seq-quality-plot_Read_1_After_filtering.pdf
│   │   │   ├── [ 14K]  fastp-seq-quality-plot_Read_1_Before_filtering.pdf
│   │   │   ├── [ 13K]  fastp-seq-quality-plot_Read_2_Before_filtering.pdf
│   │   │   ├── [ 13K]  fastqc-1_adapter_content_plot.pdf
│   │   │   ├── [ 13K]  fastqc-1_overrepresented_sequences_plot.pdf
│   │   │   ├── [ 12K]  fastqc-1_per_base_n_content_plot.pdf
│   │   │   ├── [ 13K]  fastqc-1_per_base_sequence_quality_plot.pdf
│   │   │   ├── [ 12K]  fastqc-1_per_sequence_gc_content_plot_Counts.pdf
│   │   │   ├── [ 12K]  fastqc-1_per_sequence_gc_content_plot_Percentages.pdf
│   │   │   ├── [ 12K]  fastqc-1_per_sequence_quality_scores_plot.pdf
│   │   │   ├── [ 12K]  fastqc-1_sequence_counts_plot-cnt.pdf
│   │   │   ├── [ 12K]  fastqc-1_sequence_counts_plot-pct.pdf
│   │   │   ├── [ 13K]  fastqc-1_sequence_duplication_levels_plot.pdf
│   │   │   ├── [ 13K]  fastqc-1-status-check-heatmap.pdf
│   │   │   ├── [ 15K]  fastqc-1_top_overrepresented_sequences_table.pdf
│   │   │   ├── [ 13K]  fastqc_adapter_content_plot.pdf
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│   │   │   ├── [ 13K]  fastqc_per_sequence_gc_content_plot_Counts.pdf
│   │   │   ├── [ 13K]  fastqc_per_sequence_gc_content_plot_Percentages.pdf
│   │   │   ├── [ 12K]  fastqc_per_sequence_quality_scores_plot.pdf
│   │   │   ├── [ 12K]  fastqc_sequence_counts_plot-cnt.pdf
│   │   │   ├── [ 12K]  fastqc_sequence_counts_plot-pct.pdf
│   │   │   ├── [ 13K]  fastqc_sequence_duplication_levels_plot.pdf
│   │   │   ├── [ 12K]  fastqc_sequence_length_distribution_plot.pdf
│   │   │   ├── [ 13K]  fastqc-status-check-heatmap.pdf
│   │   │   ├── [ 15K]  fastqc_top_overrepresented_sequences_table.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Class-cnt.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Class-pct.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Domain-cnt.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Domain-pct.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Family-cnt.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Family-pct.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Genus-cnt.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Genus-pct.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Kingdom-cnt.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Kingdom-pct.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Order-cnt.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Order-pct.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Phylum-cnt.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Phylum-pct.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Species-cnt.pdf
│   │   │   ├── [ 13K]  kraken-top-n-plot_Species-pct.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Unclassified-cnt.pdf
│   │   │   ├── [ 12K]  kraken-top-n-plot_Unclassified-pct.pdf
│   │   │   ├── [9.5K]  nanoq_plot_length_plot-cnt.pdf
│   │   │   ├── [ 10K]  nanoq_plot_length_plot-pct.pdf
│   │   │   ├── [9.3K]  nanoq_plot_quality_plot-cnt.pdf
│   │   │   ├── [10.0K]  nanoq_plot_quality_plot-pct.pdf
│   │   │   ├── [ 17K]  nanoq_table.pdf
│   │   │   ├── [ 35K]  nonpareil-redundancy-plot_Combined.pdf
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│   │   ├── [ 11M]  png
│   │   │   ├── [ 75K]  bbduk-filtered-barplot_Bases-cnt.png
│   │   │   ├── [ 77K]  bbduk-filtered-barplot_Bases-pct.png
│   │   │   ├── [ 81K]  bbduk-filtered-barplot_Reads-cnt.png
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│   │   │   ├── [ 79K]  bracken-top-n-plot_Class-cnt.png
│   │   │   ├── [ 71K]  bracken-top-n-plot_Class-pct.png
│   │   │   ├── [ 73K]  bracken-top-n-plot_Domain-cnt.png
│   │   │   ├── [ 66K]  bracken-top-n-plot_Domain-pct.png
│   │   │   ├── [ 80K]  bracken-top-n-plot_Family-cnt.png
│   │   │   ├── [ 71K]  bracken-top-n-plot_Family-pct.png
│   │   │   ├── [ 77K]  bracken-top-n-plot_Genus-cnt.png
│   │   │   ├── [ 69K]  bracken-top-n-plot_Genus-pct.png
│   │   │   ├── [ 75K]  bracken-top-n-plot_Kingdom-cnt.png
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│   │   │   ├── [ 80K]  bracken-top-n-plot_Order-cnt.png
│   │   │   ├── [ 71K]  bracken-top-n-plot_Order-pct.png
│   │   │   ├── [ 78K]  bracken-top-n-plot_Phylum-cnt.png
│   │   │   ├── [ 70K]  bracken-top-n-plot_Phylum-pct.png
│   │   │   ├── [ 82K]  bracken-top-n-plot_Species-cnt.png
│   │   │   ├── [ 73K]  bracken-top-n-plot_Species-pct.png
│   │   │   ├── [ 73K]  bracken-top-n-plot_Unclassified-cnt.png
│   │   │   ├── [ 67K]  bracken-top-n-plot_Unclassified-pct.png
│   │   │   ├── [ 76K]  centrifuge-top-n-plot_Class-cnt.png
│   │   │   ├── [ 68K]  centrifuge-top-n-plot_Class-pct.png
│   │   │   ├── [ 71K]  centrifuge-top-n-plot_Domain-cnt.png
│   │   │   ├── [ 65K]  centrifuge-top-n-plot_Domain-pct.png
│   │   │   ├── [ 75K]  centrifuge-top-n-plot_Family-cnt.png
│   │   │   ├── [ 68K]  centrifuge-top-n-plot_Family-pct.png
│   │   │   ├── [ 72K]  centrifuge-top-n-plot_Genus-cnt.png
│   │   │   ├── [ 66K]  centrifuge-top-n-plot_Genus-pct.png
│   │   │   ├── [ 75K]  centrifuge-top-n-plot_Kingdom-cnt.png
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│   │   │   ├── [ 76K]  centrifuge-top-n-plot_Phylum-cnt.png
│   │   │   ├── [ 69K]  centrifuge-top-n-plot_Phylum-pct.png
│   │   │   ├── [ 75K]  centrifuge-top-n-plot_Species-cnt.png
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│   │   │   ├── [ 81K]  fastp_filtered_reads_plot-cnt.png
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│   │   │   ├── [204K]  fastp-insert-size-plot.png
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│   │   │   ├── [130K]  fastp-seq-content-gc-plot_Read_1_After_filtering.png
│   │   │   ├── [163K]  fastp-seq-content-gc-plot_Read_1_Before_filtering.png
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│   │   │   ├── [114K]  fastp-seq-quality-plot_Merged_and_filtered.png
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│   │   │   ├── [132K]  fastp-seq-quality-plot_Read_2_Before_filtering.png
│   │   │   ├── [123K]  fastqc-1_adapter_content_plot.png
│   │   │   ├── [ 96K]  fastqc-1_overrepresented_sequences_plot.png
│   │   │   ├── [ 98K]  fastqc-1_per_base_n_content_plot.png
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│   │   │   ├── [164K]  fastqc-1_per_sequence_gc_content_plot_Counts.png
│   │   │   ├── [199K]  fastqc-1_per_sequence_gc_content_plot_Percentages.png
│   │   │   ├── [148K]  fastqc-1_per_sequence_quality_scores_plot.png
│   │   │   ├── [ 83K]  fastqc-1_sequence_counts_plot-cnt.png
│   │   │   ├── [ 78K]  fastqc-1_sequence_counts_plot-pct.png
│   │   │   ├── [147K]  fastqc-1_sequence_duplication_levels_plot.png
│   │   │   ├── [124K]  fastqc-1-status-check-heatmap.png
│   │   │   ├── [ 66K]  fastqc-1_top_overrepresented_sequences_table.png
│   │   │   ├── [137K]  fastqc_adapter_content_plot.png
│   │   │   ├── [125K]  fastqc_overrepresented_sequences_plot.png
│   │   │   ├── [106K]  fastqc_per_base_n_content_plot.png
│   │   │   ├── [120K]  fastqc_per_base_sequence_quality_plot.png
│   │   │   ├── [179K]  fastqc_per_sequence_gc_content_plot_Counts.png
│   │   │   ├── [225K]  fastqc_per_sequence_gc_content_plot_Percentages.png
│   │   │   ├── [161K]  fastqc_per_sequence_quality_scores_plot.png
│   │   │   ├── [109K]  fastqc_sequence_counts_plot-cnt.png
│   │   │   ├── [102K]  fastqc_sequence_counts_plot-pct.png
│   │   │   ├── [147K]  fastqc_sequence_duplication_levels_plot.png
│   │   │   ├── [123K]  fastqc_sequence_length_distribution_plot.png
│   │   │   ├── [150K]  fastqc-status-check-heatmap.png
│   │   │   ├── [ 66K]  fastqc_top_overrepresented_sequences_table.png
│   │   │   ├── [ 74K]  kraken-top-n-plot_Class-cnt.png
│   │   │   ├── [ 66K]  kraken-top-n-plot_Class-pct.png
│   │   │   ├── [ 71K]  kraken-top-n-plot_Domain-cnt.png
│   │   │   ├── [ 62K]  kraken-top-n-plot_Domain-pct.png
│   │   │   ├── [ 75K]  kraken-top-n-plot_Family-cnt.png
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│   │       ├── [9.3K]  nanoq_plot_quality_plot-cnt.svg
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│   │       ├── [ 63K]  nanoq_table.svg
│   │       ├── [ 18K]  nonpareil-redundancy-plot_Combined.svg
│   │       ├── [ 17K]  nonpareil-redundancy-plot_Model.svg
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│   │       ├── [ 59K]  nonpareil-table.svg
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│   │       └── [127K]  samtools-stats-dp.svg
│   └── [6.5M]  multiqc_report.html
├── [4.9K]  nanoq
│   └── [ 928]  ERR3201952_ERR3201952_filtered.stats
├── [3.8M]  nonpareil
│   ├── [811K]  2612_ERR5766176_B.npa
│   ├── [ 66K]  2612_ERR5766176_B.npc
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│   ├── [ 411]  nonpareil_all_samples.csv
│   ├── [190K]  nonpareil_all_samples.json
│   ├── [ 32K]  nonpareil_all_samples_mqc.png
│   ├── [ 15K]  nonpareil_all_samples.pdf
│   └── [ 388]  nonpareil_all_samples.tsv
├── [   0]  out.txt
├── [3.6M]  pipeline_info
│   ├── [3.3M]  execution_report_2025-11-04_14-25-16.html
│   ├── [305K]  execution_timeline_2025-11-04_14-25-16.html
│   ├── [ 32K]  execution_trace_2025-11-04_14-25-16.txt
│   ├── [1.6K]  nf_core_taxprofiler_software_mqc_versions.yml
│   ├── [4.9K]  params_2025-11-04_14-25-23.json
│   └── [ 14K]  pipeline_dag_2025-11-04_14-25-16.html
├── [ 79K]  porechop_abi
│   └── [ 75K]  ERR3201952_ERR3201952_porechop_abi.log
├── [9.5M]  samtools
│   ├── [ 160]  2612_ERR5766176.bam.bai
│   ├── [ 160]  2612_ERR5766176_B.bam.bai
│   ├── [ 160]  2612_ERR5766180.bam.bai
│   ├── [ 160]  2613_ERR5766181.bam.bai
│   ├── [  24]  ERR3201952_ERR3201952.bam.bai
│   ├── [5.5M]  ERR3201952_ERR3201952.unmapped.bam
│   └── [4.0M]  stats
│       ├── [ 81K]  2612_ERR5766176_B.stats
│       ├── [ 81K]  2612_ERR5766176.stats
│       ├── [ 49K]  2612_ERR5766180.stats
│       ├── [ 80K]  2613_ERR5766181.stats
│       └── [3.7M]  ERR3201952_ERR3201952.stats
└── [7.2K]  taxpasta
    ├── [  91]  bracken_db1.tsv
    ├── [ 573]  centrifuge_db3.tsv
    ├── [  94]  diamond_db1.tsv
    ├── [  65]  diamond_db2.tsv
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    ├── [  94]  ganon_db1.tsv
    ├── [ 108]  kaiju_db5.tsv
    ├── [  81]  kaiju_db6.tsv
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    ├── [ 100]  kmcp_db1.tsv
    ├── [ 647]  kraken2_db1-bracken.tsv
    ├── [ 647]  kraken2_db2.tsv
    ├── [ 146]  metaphlan_metaphlan3.tsv
    └── [ 312]  metaphlan_metaphlan4.tsv

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```