# nf-core/eager v3 docs concept


Structure: https://docs.google.com/drawings/d/14BHYl9CfhcbdlBXFvTQkE2H9WZqxjgUn7IqrVojLgA8/edit?usp=sharing

## Structure detail

Note: file patterns may not be comprehensive nor correct!

| Section | Step | Type | Files |
| --------------------- | -------------------- | ------- | ----------------------------------------- |
| `references` | `fasta` | `data` | `*.{fa,fai,dict}` |
| `references` | `bwaindex` | `data` | `*.{sa,bwt,...}` |
| `references` | `bowtie2` | `data` | `*.{btw2}` |
| `references` | `circulargenerator` | `data` | `*.{sa,bwt,...}` |
| `references` | `mapadindex` | `data` | `*.{tbw,toc,...}` |
| `preprocessing` | `bam2fastq` | `data` | `*.fastq.gz` |
| `preprocessing` | `fastqc-pre` | `stats` | `*.{html,zip}` |
| `preprocessing` | `falco-pre` | `stats` | `*.{html,zip}` |
| `preprocessing` | `fastp` | `data` | `*.fastq.gz` |
| `preprocessing` | `fastp` | `stats` | `*.{log,html,json}` |
| `preprocessing` | `adapterremoval` | `data` | `*.fastqc.gz` |
| `preprocessing` | `adapterremoval` | `stats` | `*.settings` |
| `preprocessing` | `fastqc-post` | `stats` | `*.html` |
| `preprocessing` | `falco-post` | `stats` | `*.{html,zip}` |
| `mapping` | `input_bam` | `data` | `*.{bam,bai}` |
| `mapping` | `input_bam` | `stats` | `*.flagstats` |
| `mapping` | `bwaaln` | `data` | `*.{bam,bai}` |
| `mapping` | `bwaaln` | `stats` | `*.flagstats` |
| `mapping` | `bwamem` | `data` | `*.{bam,bai}` |
| `mapping` | `bwamem` | `stats` | `*.flagstats` |
| `mapping` | `bowtie2` | `data` | `*.{bam,bai}` |
| `mapping` | `bowtie2` | `stats` | `*.flagstats` |
| `mapping` | `circularmapper` | `data` | `*.{bam,bai}` |
| `mapping` | `circularmapper` | `stats` | `*.flagstats` |
| `mapping` | `mapad` | `data` | `*.{bam,bai}` |
| `mapping` | `mapad` | `stats` | `*.flagstats` |
| `read_filtering` | `fastq` | `data` | `*.{fastq}` |
| `read_filtering` | `filtered_bams` | `data` | `*.{bam,bai}` |
| `read_filtering` | `filtered_bams` | `stats` | `*.flagstats` |
| `read_filtering` | `host_removal` | `data` | `*.fq.gz` |
| `metagenomics` | `prinseq++` | `data` | `*.fastq.gz` |
| `metagenomics` | `prinseq++` | `stats` | `*.log` |
| `metagenomics` | `bbduk` | `data` | `*.fastq.gz` |
| `metagenomics` | `bbduk` | `stats` | `*.log` |
| `metagenomics` | `malt` | `data` | `*.{rma6,sam.gz}` |
| `metagenomics` | `malt` | `stats` | `*.log` |
| `metagenomics` | `kraken2` | `data` | `*.fastq.gz` |
| `metagenomics` | `kraken2` | `stats` | `*.log` |
| `metagenomics` | `krakenuniq` | `data` | `*.fastq.gz` |
| `metagenomics` | `krakenuniq` | `stats` | `*.log` |
| `metagenomics` | `metaphlan` | `stats` | `*.{biom,txt}` |
| `metagenomics` | `maltextract` | `stats` | `results` |
| `metagenomics` | `megan_rma2info` | `stats` | `*.{txt.gz,megan}` |
| `metagenomics` | `amps` | `stats` | `results` |
| `metagenomics` | `taxpasta` | `stats` | `*.{csv,tsv,ods,xlsx,arrow,parquet,biom}` |
| `deduplication` | `dedup` | `data` | `*.{bam,bai}` |
| `deduplication` | `dedup` | `stats` | `*.flagstat` |
| `deduplication` | `markduplicates` | `data` | `*.{bam,bai}` |
| `deduplication` | `markduplicates` | `stats` | `*.flagstat` |
| `authentication` | `mapdamage2` | `stats` | `*` |
| `authentication` | `damageprofiler` | `stats` | `*.{txt,svg,pdf,log,json}` |
| `authentication` | `bedtools` | `stats` | `*.bed` |
| `authentication` | `preseq` | `stats` | `*.{txt,log}` |
| `authentication` | `qualimap` | `stats` | `*.{png,txt,html}` |
| `authentication` |`angsd_nuclear_contamination`|`stats`| `*.{txt,json}` |
| `authentication` | `sexdeterrmine` | `stats` | `*.{tsv,json}` |
| `authentication` | `endorspy` | `stats` | `*.{tsv,json}` |
| `damage_manipulation` | `mapdamage2` | `data` | `*.{bam,bai}` |
| `damage_manipulation` | `mapdamage2` | `stats` | `*.{pdf,csv}` |
| `damage_manipulation` | `pmdtools` | `data` | `*.{bam,bai}` |
| `damage_manipulation` | `bamutils_trimbam` | `data` | `*.{bam,bai}` |
| `final_bams` | `$genotyping_source` | `data` | `*.{bam,bai}` |
| `final_bams` | `$genotyping_source` | `stats` | `*.flagstat` |
| `genotyping` | `pileupcaller` | `data` | `*.{geno,snp,ind}` |
| `genotyping` | `pileupcaller` | `stats` | `*.{txt,json}` |
| `genotyping` | `gatk_ug` | `data` | `*.vcf.gz{,.tbi}` |
| `genotyping` | `gatk_hc` | `data` | `*.vcf.gz{,.tbi}` |
| `genotyping` | `freebayes` | `data` | `*.vcf.gz{,.tbi}` |
| `genotyping` | `angsd` | `data` | `*.{glf,beagle}.gz` |
| `genotyping` | `bcftools` | `stats` | `*.txt` |
| `multiqc` | NA | NA | `{*.html,multiqc_data/*}` |

| `consensus_calling` |
| `multiqc` | NA | NA | `*.html`

Possible dynamic:

- endorSpy