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‎docs/tools/metadata.md

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# seqfu metadata
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Given one (or more) directories containing sequencing reads,
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will produce a metadata file extracting the ID from the filename
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and optionally adding the file paths or read counts.
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Given one (or more) directories containing sequencing reads, this tool produces a metadata file by extracting the ID from the filename and optionally adding file paths or read counts.
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## Usage
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```
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Usage: metadata [options] [<dir>...]
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metadata formats
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Prepare mapping files from directory containing FASTQ files
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-s, --split STR Separator used in filename to identify the sample ID [default: _]
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--pos INT... Which part of the filename is the Sample ID [default: 1]
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-f, --format TYPE Output format: dadaist, irida, manifest, metaphage, qiime1, qiime2 [default: manifest]
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--pe Enforce paired-end reads (not supported)
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-f, --format TYPE Output format: dadaist, irida, manifest, metaphage, qiime1, qiime2, lotus, ampliseq, rnaseq, bactopia, mag [default: manifest]
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-p, --add-path Add the reads absolute path as column
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-c, --counts Add the number of reads as a property column
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-t, --threads INT Number of simultaneously opened files [default: 2]
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-c, --counts Add the number of reads as a property column (experimental)
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-t, --threads INT Number of simultaneously opened files (legacy: ignored)
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--pe Enforce paired-end reads (not supported)
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--ont Long reads (Oxford Nanopore) [default: false]
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GLOBAL OPTIONS
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--abs Force absolute path
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--basename Use basename instead of full path
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--force-tsv Force '\t' separator, otherwise selected by the format
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--force-csv Force ',' separator, otherwise selected by the format
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-R, --rand-meta INT Add a random metadata column with INT categories
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FORMAT SPECIFIC OPTIONS
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-P, --project INT Project ID (only for irida)
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--meta-default STR Default value for metadata, used in MetaPhage [default: Cond]
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-v, --verbose Verbose output
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--debug Debug output
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-h, --help Show this help
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```
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## Output formats
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* manifest (used as import manifest for [Qiime2](https://qiime2.org/) artifacts)
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* qiime1, qiime2 (forward-compatible [qiime1](http://qiime.org/) mapping file; a dedicated [Qiime2](https://qiime2.org/) metadata file is under development)
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* dadaist ([Dadaist2](quadram-institute-bioscience.github.io/dadaist2) compatible metadata)
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* lotus ([Lotus](http://lotus2.earlham.ac.uk/) mapping file - tested with Lotus1)
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* irida ([IRIDA uploader](https://github.com/phac-nml/irida-uploader) sample sheet. Requires `-P PROJECTID`)
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* metaphage ([MetaPhage](https://mattiapandolfovr.github.io/MetaPhage), use `--meta-split`, `--meta-part` and `--meta-default` to customize a Treatment column)
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SeqFu metadata now supports the following output formats:
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1. **manifest**: Used as import manifest for [Qiime2](https://qiime2.org/) artifacts.
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2. **qiime1**: Forward-compatible [Qiime1](http://qiime.org/) mapping file.
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3. **qiime2**: [Qiime2](https://qiime2.org/) metadata file.
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4. **dadaist**: [Dadaist2](https://quadram-institute-bioscience.github.io/dadaist2) compatible metadata.
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5. **lotus**: [Lotus](http://lotus2.earlham.ac.uk/) mapping file (tested with Lotus1).
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6. **irida**: [IRIDA uploader](https://github.com/phac-nml/irida-uploader) sample sheet. Requires `-P PROJECTID`.
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7. **metaphage**: [MetaPhage](https://mattiapandolfovr.github.io/MetaPhage) metadata file. Use `--meta-split`, `--meta-part`, and `--meta-default` to customize a Treatment column.
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8. **ampliseq**: [nf-core/ampliseq](https://nf-co.re/ampliseq) metadata file.
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9. **rnaseq**: [nf-core/rnaseq](https://nf-co.re/rnaseq) metadata file.
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10. **bactopia**: [Bactopia](https://bactopia.github.io/) FOFN (File of File Names) file.
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11. **mag**: [nf-core/mag](https://nf-co.re/mag) metadata file.
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## New Features
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- Support for `--format bactopia` to generate Bactopia FOFN files.
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- Added `--ont` option for long reads (Oxford Nanopore Technology).
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- Enhanced support for various bioinformatics pipelines (ampliseq, rnaseq, mag).
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## Examples
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### Manifest
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### Manifest (default)
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```
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```bash
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seqfu metadata ./MiSeq_SOP/
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```
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Will produce this output:
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Output:
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```
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sample-id forward-absolute-filepath reverse-absolute-filepath
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F3D0 /Users/telatin/MiSeq_SOP/F3D0_S188_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D0_S188_L001_R2_001.fastq.gz
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F3D1 /Users/telatin/MiSeq_SOP/F3D1_S189_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D1_S189_L001_R2_001.fastq.gz
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F3D141 /Users/telatin/MiSeq_SOP/F3D141_S207_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D141_S207_L001_R2_001.fastq.gz
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F3D142 /Users/telatin/MiSeq_SOP/F3D142_S208_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D142_S208_L001_R2_001.fastq.gz
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F3D143 /Users/telatin/MiSeq_SOP/F3D143_S209_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D143_S209_L001_R2_001.fastq.gz
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F3D144 /Users/telatin/MiSeq_SOP/F3D144_S210_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D144_S210_L001_R2_001.fastq.gz
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F3D145 /Users/telatin/MiSeq_SOP/F3D145_S211_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D145_S211_L001_R2_001.fastq.gz
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F3D146 /Users/telatin/MiSeq_SOP/F3D146_S212_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D146_S212_L001_R2_001.fastq.gz
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F3D147 /Users/telatin/MiSeq_SOP/F3D147_S213_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D147_S213_L001_R2_001.fastq.gz
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F3D148 /Users/telatin/MiSeq_SOP/F3D148_S214_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D148_S214_L001_R2_001.fastq.gz
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F3D149 /Users/telatin/MiSeq_SOP/F3D149_S215_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D149_S215_L001_R2_001.fastq.gz
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F3D150 /Users/telatin/MiSeq_SOP/F3D150_S216_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D150_S216_L001_R2_001.fastq.gz
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F3D2 /Users/telatin/MiSeq_SOP/F3D2_S190_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D2_S190_L001_R2_001.fastq.gz
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F3D3 /Users/telatin/MiSeq_SOP/F3D3_S191_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D3_S191_L001_R2_001.fastq.gz
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F3D5 /Users/telatin/MiSeq_SOP/F3D5_S193_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D5_S193_L001_R2_001.fastq.gz
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F3D6 /Users/telatin/MiSeq_SOP/F3D6_S194_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D6_S194_L001_R2_001.fastq.gz
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F3D7 /Users/telatin/MiSeq_SOP/F3D7_S195_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D7_S195_L001_R2_001.fastq.gz
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F3D8 /Users/telatin/MiSeq_SOP/F3D8_S196_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D8_S196_L001_R2_001.fastq.gz
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F3D9 /Users/telatin/MiSeq_SOP/F3D9_S197_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D9_S197_L001_R2_001.fastq.gz
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Mock /Users/telatin/MiSeq_SOP/Mock_S280_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/Mock_S280_L001_R2_001.fastq.gz
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...
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```
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### Qiime mapping file
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Note that `-f qiime2` will add a second header line.
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### Qiime1 mapping file
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```
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```bash
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seqfu metadata MiSeq_SOP -f qiime1 --add-path --counts
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```
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Output:
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```
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#SampleID Counts Paths
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F3D0 7793 F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz
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F3D1 5869 F3D1_S189_L001_R1_001.fastq.gz,F3D1_S189_L001_R2_001.fastq.gz
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F3D141 5958 F3D141_S207_L001_R1_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz
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F3D142 3183 F3D142_S208_L001_R1_001.fastq.gz,F3D142_S208_L001_R2_001.fastq.gz
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F3D143 3178 F3D143_S209_L001_R1_001.fastq.gz,F3D143_S209_L001_R2_001.fastq.gz
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F3D144 4827 F3D144_S210_L001_R1_001.fastq.gz,F3D144_S210_L001_R2_001.fastq.gz
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F3D145 7377 F3D145_S211_L001_R1_001.fastq.gz,F3D145_S211_L001_R2_001.fastq.gz
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F3D146 5021 F3D146_S212_L001_R1_001.fastq.gz,F3D146_S212_L001_R2_001.fastq.gz
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F3D147 17070 F3D147_S213_L001_R1_001.fastq.gz,F3D147_S213_L001_R2_001.fastq.gz
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F3D148 12405 F3D148_S214_L001_R1_001.fastq.gz,F3D148_S214_L001_R2_001.fastq.gz
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F3D149 13083 F3D149_S215_L001_R1_001.fastq.gz,F3D149_S215_L001_R2_001.fastq.gz
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F3D150 5509 F3D150_S216_L001_R1_001.fastq.gz,F3D150_S216_L001_R2_001.fastq.gz
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F3D2 19620 F3D2_S190_L001_R1_001.fastq.gz,F3D2_S190_L001_R2_001.fastq.gz
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F3D3 6758 F3D3_S191_L001_R1_001.fastq.gz,F3D3_S191_L001_R2_001.fastq.gz
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F3D5 4448 F3D5_S193_L001_R1_001.fastq.gz,F3D5_S193_L001_R2_001.fastq.gz
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F3D6 7989 F3D6_S194_L001_R1_001.fastq.gz,F3D6_S194_L001_R2_001.fastq.gz
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F3D7 5129 F3D7_S195_L001_R1_001.fastq.gz,F3D7_S195_L001_R2_001.fastq.gz
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F3D8 5294 F3D8_S196_L001_R1_001.fastq.gz,F3D8_S196_L001_R2_001.fastq.gz
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F3D9 7070 F3D9_S197_L001_R1_001.fastq.gz,F3D9_S197_L001_R2_001.fastq.gz
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Mock 4779 Mock_S280_L001_R1_001.fastq.gz,Mock_S280_L001_R2_001.fastq.gz
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...
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```
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### IRIDA uploader
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```
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seqfu metadata -f irida -P 123 data/pe/
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```bash
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seqfu metadata -f irida -P 123 data/pe/
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```
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Output:
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sample2,123,sample2_R1.fq.gz,sample2_R2.fq.gz
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```
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### Bactopia FOFN
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```bash
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seqfu metadata -f bactopia data/pe/
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```
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Output:
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```
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sample runtype r1 r2
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sample1 paired-end /path/to/data/pe/sample1_R1.fq.gz /path/to/data/pe/sample1_R2.fq.gz
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sample2 paired-end /path/to/data/pe/sample2_R1.fq.gz /path/to/data/pe/sample2_R2.fq.gz
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```
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## Notes
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## Screenshot
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- The `--ont` option is useful for projects involving Oxford Nanopore long reads.
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- Use `--add-path` to include full file paths in the output (when supported by the format).
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- The `--counts` option adds read counts to the output (experimental feature, not supported by all formats).
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- Format-specific options (like `--project` for IRIDA) are required for certain output types.
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- Use `--verbose` for detailed processing information and `--debug` for troubleshooting.
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![Screenshot of "seqfu metadata"]({{site.baseurl}}/img/screenshot-metadata.svg "SeqFu metadata")
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For more information on each format and its specific options, please refer to the respective tool's documentation.

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