# 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
│ │ ├── [ 98] kraken-top-n-plot_Unclassified.txt
│ │ ├── [278K] llms-full.txt
│ │ ├── [ 288] metaphlan-top-n-plot_Class.txt
│ │ ├── [ 293] metaphlan-top-n-plot_Family.txt
│ │ ├── [ 290] metaphlan-top-n-plot_Genus.txt
│ │ ├── [ 286] metaphlan-top-n-plot_Kingdom.txt
│ │ ├── [ 291] metaphlan-top-n-plot_Order.txt
│ │ ├── [ 288] metaphlan-top-n-plot_Phylum.txt
│ │ ├── [ 297] metaphlan-top-n-plot_Species.txt
│ │ ├── [ 307] multiqc_bowtie2.txt
│ │ ├── [1.1K] multiqc_bracken_bracken.txt
│ │ ├── [ 732] multiqc_centrifuge_centrifuge.txt
│ │ ├── [ 793] multiqc_citations.txt
│ │ ├── [6.8M] multiqc_data.json
│ │ ├── [397K] multiqc_fastp.txt
│ │ ├── [1.5K] multiqc_fastqc_fastqc-1.txt
│ │ ├── [2.1K] multiqc_fastqc.txt
│ │ ├── [8.8K] multiqc_general_stats.txt
│ │ ├── [ 335] multiqc_kaiju_species.txt
│ │ ├── [1.0K] multiqc_kraken.txt
│ │ ├── [ 93K] multiqc.log
│ │ ├── [1.2K] multiqc_metaphlan.txt
│ │ ├── [ 549] multiqc_nanoq.txt
│ │ ├── [199K] multiqc_nonpareil.txt
│ │ ├── [4.2M] multiqc.parquet
│ │ ├── [2.5K] multiqc_samtools_stats.txt
│ │ ├── [2.4K] multiqc_software_versions.txt
│ │ ├── [ 11K] multiqc_sources.txt
│ │ ├── [ 133] nanoq_plot_length_plot.txt
│ │ ├── [ 101] nanoq_plot_quality_plot.txt
│ │ ├── [ 212] nanoq_table.txt
│ │ ├── [101K] nonpareil-redundancy-plot_Combined.txt
│ │ ├── [ 50K] nonpareil-redundancy-plot_Model.txt
│ │ ├── [3.0K] nonpareil-redundancy-plot_Observed.txt
│ │ ├── [ 695] nonpareil-table.txt
│ │ ├── [ 58] porechop-endtrim-barplot.txt
│ │ ├── [ 55] porechop-middlesplit-barplot.txt
│ │ ├── [ 392] porechop_porechop_abi.txt
│ │ ├── [ 62] porechop-starttrim-barplot.txt
│ │ ├── [ 214] samtools_alignment_plot.txt
│ │ └── [ 699] samtools-stats-dp.txt
│ ├── [ 14M] multiqc_plots
│ │ ├── [1.5M] pdf
│ │ │ ├── [ 12K] bbduk-filtered-barplot_Bases-cnt.pdf
│ │ │ ├── [ 12K] bbduk-filtered-barplot_Bases-pct.pdf
│ │ │ ├── [ 12K] bbduk-filtered-barplot_Reads-cnt.pdf
│ │ │ ├── [ 12K] bbduk-filtered-barplot_Reads-pct.pdf
│ │ │ ├── [ 12K] bowtie2_se_plot-cnt.pdf
│ │ │ ├── [ 12K] bowtie2_se_plot-pct.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Class-cnt.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Class-pct.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Domain-cnt.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Domain-pct.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Family-cnt.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Family-pct.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Genus-cnt.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Genus-pct.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Kingdom-cnt.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Kingdom-pct.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Order-cnt.pdf
│ │ │ ├── [ 12K] bracken-top-n-plot_Order-pct.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Phylum-cnt.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Phylum-pct.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Species-cnt.pdf
│ │ │ ├── [ 13K] bracken-top-n-plot_Species-pct.pdf
│ │ │ ├── [ 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
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Family-cnt.pdf
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Family-pct.pdf
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Genus-cnt.pdf
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Genus-pct.pdf
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Kingdom-cnt.pdf
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Kingdom-pct.pdf
│ │ │ ├── [ 12K] centrifuge-top-n-plot_Order-cnt.pdf
│ │ │ ├── [ 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
│ │ │ ├── [ 13K] fastp_filtered_reads_plot-pct.pdf
│ │ │ ├── [ 14K] fastp-insert-size-plot.pdf
│ │ │ ├── [ 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
│ │ │ ├── [ 13K] fastqc_overrepresented_sequences_plot.pdf
│ │ │ ├── [ 12K] fastqc_per_base_n_content_plot.pdf
│ │ │ ├── [ 12K] fastqc_per_base_sequence_quality_plot.pdf
│ │ │ ├── [ 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
│ │ │ ├── [ 14K] nonpareil-redundancy-plot_Model.pdf
│ │ │ ├── [ 14K] nonpareil-redundancy-plot_Observed.pdf
│ │ │ ├── [ 21K] nonpareil-table.pdf
│ │ │ ├── [ 11K] porechop-endtrim-barplot-cnt.pdf
│ │ │ ├── [ 11K] porechop-endtrim-barplot-pct.pdf
│ │ │ ├── [ 11K] porechop-middlesplit-barplot-cnt.pdf
│ │ │ ├── [ 11K] porechop-middlesplit-barplot-pct.pdf
│ │ │ ├── [ 11K] porechop-starttrim-barplot-cnt.pdf
│ │ │ ├── [ 11K] porechop-starttrim-barplot-pct.pdf
│ │ │ ├── [ 13K] samtools_alignment_plot-cnt.pdf
│ │ │ ├── [ 13K] samtools_alignment_plot-pct.pdf
│ │ │ └── [ 26K] samtools-stats-dp.pdf
│ │ ├── [ 11M] png
│ │ │ ├── [ 75K] bbduk-filtered-barplot_Bases-cnt.png
│ │ │ ├── [ 77K] bbduk-filtered-barplot_Bases-pct.png
│ │ │ ├── [ 81K] bbduk-filtered-barplot_Reads-cnt.png
│ │ │ ├── [ 76K] bbduk-filtered-barplot_Reads-pct.png
│ │ │ ├── [ 81K] bowtie2_se_plot-cnt.png
│ │ │ ├── [ 77K] bowtie2_se_plot-pct.png
│ │ │ ├── [ 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
│ │ │ ├── [ 69K] bracken-top-n-plot_Kingdom-pct.png
│ │ │ ├── [ 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
│ │ │ ├── [ 68K] centrifuge-top-n-plot_Kingdom-pct.png
│ │ │ ├── [ 74K] centrifuge-top-n-plot_Order-cnt.png
│ │ │ ├── [ 67K] centrifuge-top-n-plot_Order-pct.png
│ │ │ ├── [ 76K] centrifuge-top-n-plot_Phylum-cnt.png
│ │ │ ├── [ 69K] centrifuge-top-n-plot_Phylum-pct.png
│ │ │ ├── [ 75K] centrifuge-top-n-plot_Species-cnt.png
│ │ │ ├── [ 70K] centrifuge-top-n-plot_Species-pct.png
│ │ │ ├── [ 81K] fastp_filtered_reads_plot-cnt.png
│ │ │ ├── [ 79K] fastp_filtered_reads_plot-pct.png
│ │ │ ├── [204K] fastp-insert-size-plot.png
│ │ │ ├── [146K] fastp-seq-content-gc-plot_Merged_and_filtered.png
│ │ │ ├── [130K] fastp-seq-content-gc-plot_Read_1_After_filtering.png
│ │ │ ├── [163K] fastp-seq-content-gc-plot_Read_1_Before_filtering.png
│ │ │ ├── [146K] fastp-seq-content-gc-plot_Read_2_Before_filtering.png
│ │ │ ├── [ 96K] fastp-seq-content-n-plot_Merged_and_filtered.png
│ │ │ ├── [107K] fastp-seq-content-n-plot_Read_1_After_filtering.png
│ │ │ ├── [117K] fastp-seq-content-n-plot_Read_1_Before_filtering.png
│ │ │ ├── [116K] fastp-seq-content-n-plot_Read_2_Before_filtering.png
│ │ │ ├── [114K] fastp-seq-quality-plot_Merged_and_filtered.png
│ │ │ ├── [114K] fastp-seq-quality-plot_Read_1_After_filtering.png
│ │ │ ├── [141K] fastp-seq-quality-plot_Read_1_Before_filtering.png
│ │ │ ├── [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
│ │ │ ├── [118K] fastqc-1_per_base_sequence_quality_plot.png
│ │ │ ├── [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
│ │ │ ├── [ 67K] kraken-top-n-plot_Family-pct.png
│ │ │ ├── [ 74K] kraken-top-n-plot_Genus-cnt.png
│ │ │ ├── [ 66K] kraken-top-n-plot_Genus-pct.png
│ │ │ ├── [ 73K] kraken-top-n-plot_Kingdom-cnt.png
│ │ │ ├── [ 64K] kraken-top-n-plot_Kingdom-pct.png
│ │ │ ├── [ 74K] kraken-top-n-plot_Order-cnt.png
│ │ │ ├── [ 67K] kraken-top-n-plot_Order-pct.png
│ │ │ ├── [ 74K] kraken-top-n-plot_Phylum-cnt.png
│ │ │ ├── [ 65K] kraken-top-n-plot_Phylum-pct.png
│ │ │ ├── [ 78K] kraken-top-n-plot_Species-cnt.png
│ │ │ ├── [ 69K] kraken-top-n-plot_Species-pct.png
│ │ │ ├── [ 70K] kraken-top-n-plot_Unclassified-cnt.png
│ │ │ ├── [ 62K] kraken-top-n-plot_Unclassified-pct.png
│ │ │ ├── [ 68K] nanoq_plot_length_plot-cnt.png
│ │ │ ├── [ 69K] nanoq_plot_length_plot-pct.png
│ │ │ ├── [ 63K] nanoq_plot_quality_plot-cnt.png
│ │ │ ├── [ 64K] nanoq_plot_quality_plot-pct.png
│ │ │ ├── [144K] nanoq_table.png
│ │ │ ├── [143K] nonpareil-redundancy-plot_Combined.png
│ │ │ ├── [141K] nonpareil-redundancy-plot_Model.png
│ │ │ ├── [117K] nonpareil-redundancy-plot_Observed.png
│ │ │ ├── [125K] nonpareil-table.png
│ │ │ ├── [ 61K] porechop-endtrim-barplot-cnt.png
│ │ │ ├── [ 58K] porechop-endtrim-barplot-pct.png
│ │ │ ├── [ 58K] porechop-middlesplit-barplot-cnt.png
│ │ │ ├── [ 56K] porechop-middlesplit-barplot-pct.png
│ │ │ ├── [ 63K] porechop-starttrim-barplot-cnt.png
│ │ │ ├── [ 61K] porechop-starttrim-barplot-pct.png
│ │ │ ├── [ 85K] samtools_alignment_plot-cnt.png
│ │ │ ├── [ 81K] samtools_alignment_plot-pct.png
│ │ │ └── [249K] samtools-stats-dp.png
│ │ └── [1.6M] svg
│ │ ├── [9.7K] bbduk-filtered-barplot_Bases-cnt.svg
│ │ ├── [9.5K] bbduk-filtered-barplot_Bases-pct.svg
│ │ ├── [ 11K] bbduk-filtered-barplot_Reads-cnt.svg
│ │ ├── [9.5K] bbduk-filtered-barplot_Reads-pct.svg
│ │ ├── [ 12K] bowtie2_se_plot-cnt.svg
│ │ ├── [ 11K] bowtie2_se_plot-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Class-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Class-pct.svg
│ │ ├── [ 11K] bracken-top-n-plot_Domain-cnt.svg
│ │ ├── [8.9K] bracken-top-n-plot_Domain-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Family-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Family-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Genus-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Genus-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Kingdom-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Kingdom-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Order-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Order-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Phylum-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Phylum-pct.svg
│ │ ├── [ 12K] bracken-top-n-plot_Species-cnt.svg
│ │ ├── [ 10K] bracken-top-n-plot_Species-pct.svg
│ │ ├── [ 11K] bracken-top-n-plot_Unclassified-cnt.svg
│ │ ├── [8.9K] bracken-top-n-plot_Unclassified-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Class-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Class-pct.svg
│ │ ├── [ 10K] centrifuge-top-n-plot_Domain-cnt.svg
│ │ ├── [8.3K] centrifuge-top-n-plot_Domain-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Family-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Family-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Genus-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Genus-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Kingdom-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Kingdom-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Order-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Order-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Phylum-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Phylum-pct.svg
│ │ ├── [ 11K] centrifuge-top-n-plot_Species-cnt.svg
│ │ ├── [9.4K] centrifuge-top-n-plot_Species-pct.svg
│ │ ├── [ 16K] fastp_filtered_reads_plot-cnt.svg
│ │ ├── [ 15K] fastp_filtered_reads_plot-pct.svg
│ │ ├── [ 18K] fastp-insert-size-plot.svg
│ │ ├── [ 18K] fastp-seq-content-gc-plot_Merged_and_filtered.svg
│ │ ├── [ 10K] fastp-seq-content-gc-plot_Read_1_After_filtering.svg
│ │ ├── [ 16K] fastp-seq-content-gc-plot_Read_1_Before_filtering.svg
│ │ ├── [ 14K] fastp-seq-content-gc-plot_Read_2_Before_filtering.svg
│ │ ├── [9.2K] fastp-seq-content-n-plot_Merged_and_filtered.svg
│ │ ├── [9.1K] fastp-seq-content-n-plot_Read_1_After_filtering.svg
│ │ ├── [ 14K] fastp-seq-content-n-plot_Read_1_Before_filtering.svg
│ │ ├── [ 13K] fastp-seq-content-n-plot_Read_2_Before_filtering.svg
│ │ ├── [ 14K] fastp-seq-quality-plot_Merged_and_filtered.svg
│ │ ├── [ 11K] fastp-seq-quality-plot_Read_1_After_filtering.svg
│ │ ├── [ 16K] fastp-seq-quality-plot_Read_1_Before_filtering.svg
│ │ ├── [ 14K] fastp-seq-quality-plot_Read_2_Before_filtering.svg
│ │ ├── [ 12K] fastqc-1_adapter_content_plot.svg
│ │ ├── [ 10K] fastqc-1_overrepresented_sequences_plot.svg
│ │ ├── [ 11K] fastqc-1_per_base_n_content_plot.svg
│ │ ├── [ 14K] fastqc-1_per_base_sequence_quality_plot.svg
│ │ ├── [ 12K] fastqc-1_per_sequence_gc_content_plot_Counts.svg
│ │ ├── [ 13K] fastqc-1_per_sequence_gc_content_plot_Percentages.svg
│ │ ├── [ 14K] fastqc-1_per_sequence_quality_scores_plot.svg
│ │ ├── [ 11K] fastqc-1_sequence_counts_plot-cnt.svg
│ │ ├── [ 10K] fastqc-1_sequence_counts_plot-pct.svg
│ │ ├── [ 13K] fastqc-1_sequence_duplication_levels_plot.svg
│ │ ├── [ 11K] fastqc-1-status-check-heatmap.svg
│ │ ├── [ 27K] fastqc-1_top_overrepresented_sequences_table.svg
│ │ ├── [ 18K] fastqc_adapter_content_plot.svg
│ │ ├── [ 12K] fastqc_overrepresented_sequences_plot.svg
│ │ ├── [ 14K] fastqc_per_base_n_content_plot.svg
│ │ ├── [ 15K] fastqc_per_base_sequence_quality_plot.svg
│ │ ├── [ 15K] fastqc_per_sequence_gc_content_plot_Counts.svg
│ │ ├── [ 16K] fastqc_per_sequence_gc_content_plot_Percentages.svg
│ │ ├── [ 14K] fastqc_per_sequence_quality_scores_plot.svg
│ │ ├── [ 13K] fastqc_sequence_counts_plot-cnt.svg
│ │ ├── [ 12K] fastqc_sequence_counts_plot-pct.svg
│ │ ├── [ 14K] fastqc_sequence_duplication_levels_plot.svg
│ │ ├── [9.7K] fastqc_sequence_length_distribution_plot.svg
│ │ ├── [ 12K] fastqc-status-check-heatmap.svg
│ │ ├── [ 28K] fastqc_top_overrepresented_sequences_table.svg
│ │ ├── [ 12K] kraken-top-n-plot_Class-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Class-pct.svg
│ │ ├── [ 11K] kraken-top-n-plot_Domain-cnt.svg
│ │ ├── [8.9K] kraken-top-n-plot_Domain-pct.svg
│ │ ├── [ 12K] kraken-top-n-plot_Family-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Family-pct.svg
│ │ ├── [ 12K] kraken-top-n-plot_Genus-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Genus-pct.svg
│ │ ├── [ 12K] kraken-top-n-plot_Kingdom-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Kingdom-pct.svg
│ │ ├── [ 12K] kraken-top-n-plot_Order-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Order-pct.svg
│ │ ├── [ 12K] kraken-top-n-plot_Phylum-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Phylum-pct.svg
│ │ ├── [ 12K] kraken-top-n-plot_Species-cnt.svg
│ │ ├── [ 10K] kraken-top-n-plot_Species-pct.svg
│ │ ├── [ 11K] kraken-top-n-plot_Unclassified-cnt.svg
│ │ ├── [8.9K] kraken-top-n-plot_Unclassified-pct.svg
│ │ ├── [ 10K] nanoq_plot_length_plot-cnt.svg
│ │ ├── [ 10K] nanoq_plot_length_plot-pct.svg
│ │ ├── [9.3K] nanoq_plot_quality_plot-cnt.svg
│ │ ├── [9.2K] nanoq_plot_quality_plot-pct.svg
│ │ ├── [ 63K] nanoq_table.svg
│ │ ├── [ 18K] nonpareil-redundancy-plot_Combined.svg
│ │ ├── [ 17K] nonpareil-redundancy-plot_Model.svg
│ │ ├── [ 12K] nonpareil-redundancy-plot_Observed.svg
│ │ ├── [ 59K] nonpareil-table.svg
│ │ ├── [9.5K] porechop-endtrim-barplot-cnt.svg
│ │ ├── [7.5K] porechop-endtrim-barplot-pct.svg
│ │ ├── [9.5K] porechop-middlesplit-barplot-cnt.svg
│ │ ├── [7.5K] porechop-middlesplit-barplot-pct.svg
│ │ ├── [9.5K] porechop-starttrim-barplot-cnt.svg
│ │ ├── [7.5K] porechop-starttrim-barplot-pct.svg
│ │ ├── [ 13K] samtools_alignment_plot-cnt.svg
│ │ ├── [ 12K] samtools_alignment_plot-pct.svg
│ │ └── [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
│ ├── [2.0K] 2612_ERR5766176_B.npl
│ ├── [1.7K] 2612_ERR5766176_B.npo
│ ├── [ 23K] 2612_ERR5766176_B.png
│ ├── [811K] 2612_ERR5766176.npa
│ ├── [ 66K] 2612_ERR5766176.npc
│ ├── [2.0K] 2612_ERR5766176.npl
│ ├── [1.7K] 2612_ERR5766176.npo
│ ├── [ 23K] 2612_ERR5766176.png
│ ├── [855K] 2612_ERR5766180.npa
│ ├── [ 62K] 2612_ERR5766180.npc
│ ├── [2.1K] 2612_ERR5766180.npl
│ ├── [1.8K] 2612_ERR5766180.npo
│ ├── [ 23K] 2612_ERR5766180.png
│ ├── [811K] 2613_ERR5766181.npa
│ ├── [ 63K] 2613_ERR5766181.npc
│ ├── [2.0K] 2613_ERR5766181.npl
│ ├── [1.7K] 2613_ERR5766181.npo
│ ├── [ 23K] 2613_ERR5766181.png
│ ├── [ 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
├── [ 146] diamond_db3.tsv
├── [ 94] ganon_db1.tsv
├── [ 108] kaiju_db5.tsv
├── [ 81] kaiju_db6.tsv
├── [ 169] kaiju_db7.tsv
├── [ 100] kmcp_db1.tsv
├── [ 647] kraken2_db1-bracken.tsv
├── [ 647] kraken2_db2.tsv
├── [ 146] metaphlan_metaphlan3.tsv
└── [ 312] metaphlan_metaphlan4.tsv
1.6G used in 44 directories, 684 files
```
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