Expose all parameters from individual tools in somatem

[ppreshant]

Context:

Currently, we only implement a few (maybe important ones?) parameters for starters, but we want to provide the users with all parameters so that omi can help users set them with full flexibility.

Example

lemur has only these subset of parameters currently in nextflow.config

    // LEMUR-MAGNET
    lemur_db                   = "${params.db_base_dir}/lemur_221_db/"
    lemur_db_zenodo_id         = 10802546
    lemur_taxonomy             = "${params.lemur_db}/taxonomy.tsv"
    rank                       = "species"

and modules.config

withName: 'LEMUR' {
        ext.args = [
            "--rank ${params.rank}",
            // "--db-prefix ${params.lemur_db}", // using db-prefix directory as input
            "--tax-path ${params.lemur_taxonomy}",
        ].join(' ')                                                           // Join converts the list here to a string.
    }

And we need to include many more to make it comprehensive!

Questions

• Decide between these 2 organizations of the parameters
  • Have all parameters in one place for ease of access and understanding
  • Have current/key ones in the nextflow.config and put the rest of the parameters in a new parameters.config file. reduces clutter for those setting the pipeline manually?

Plan

1. Setup the organization for the parameters.
   • (Start with a detailed_params.config file) Decide on a config file structure for major vs minor parameters.
   • make a scheme to translate tool's param into somatem's such as tool_param
2. Work one module at a time to add all parameters included in the underlying tool to a config file.
   • Copy and load the README.md files from the omi-web-app repo to get help from AI.
   • Cut and paste the parameters into a parameters/tool.md file so we can organize it in omi-web-app at the same time!
3. Wire it up to the tool's ext.arg in modules.config
4. Test by running stub and checking log?
5. Fix old parameters that don't abide by the naming convention: tool_param

[ppreshant]

Notes

Tool migrations

• NanoPlot: keyword: # Usage.
• hostile: keyword: # Usage and/till # parameters
• chopper: # usage
• Emu: migrated, tested.
• Lemur: migrated, tested
  • stub, printing args to a txt file
  • before: --rank species --tax-path /home/dbs/lemur_221_db//taxonomy.tsv
  • After: --tax-path /home/dbs/lemur_221_db//taxonomy.tsv --num-threads 4 --aln-score AS --rank species --min-aln-len-ratio 0.75 --min-fidelity log(0.5) --ref-weight 1.0 --mm2-N 50 --mm2-K 500M --mm2-type map-ont
  • (fixed) Error while testing : seems to be with some failing simlink to the example file provided. but minimap seems to have run so not sure how it errors in the middle?
• MAGnet: # getting started
• Sylph: cookbook
• taxburst : missing readme ;
• Flye ... to be updated..
• minimap2
• samtools
• SemiBin2
• CheckM2
• SingleM pipe
• bakta
• SingleM appraise
• rhea
• MetagenomeScope
• SeqScreen
• multiqc

Parameter_migration_plan.md:

• Generated a draft from 2 iterations of chat with Windsurf: Kimi k2.5 ; executing plan with the free SWE-1.5
• Edits by hand: ignore input, output and DB path params (already covered in module)
  • add sh to code blocks
• part b: tried automating with scripts. failed..
• Do it with windsurf AI for these files: Emu, Hostile, Rhea (with manual review..)

RAG_docs_exchange$ rg -i "#.*param" githubs/
githubs/Rhea_README.md
78:### Parameters

githubs/Hostile_README.md
330:## Alignment parameters

githubs/Lemur_README.md
65:### Parameter descriptions

githubs/Emu_README.md
88:### Abundance Estimation Parameters

• Some tools contain a Usage section with similar information. example: Nanoplot
  • checkM2's usage is descriptive and lacks the CLI -h parameters (Add manually)

~/somatem/docs/somatem-docs/RAG_docs_exchange/githubs$ rg -i ^#.*(parameter|usage) ./
./Chopper_README.md
29:## Usage

./Lemur_README.md
20:## Usage
22:### Basic usage
65:### Parameter descriptions

./Rhea_README.md
78:### Parameters

./NanoPlot_README.md
47:### USAGE
143:### EXAMPLE USAGE

./Hostile_README.md
99:## Command line usage
284:## Python usage
330:## Alignment parameters

./CheckM2_README.md
8:# Usage

./SemiBin_README.md
24:## Basic usage of SemiBin

./Bakta_README.md
376:## Usage
686:### Usage
734:### Usage

./Emu_README.md
88:### Abundance Estimation Parameters

[ppreshant]

Notes:

• Lemur: (fixed with simple typo in file path that is not noticable) Short error: (see below for long error)

  ERROR: failed to open file 'example.fastq': No such file or directory
  ERROR: failed to map the query file

Lemur testing longer error:

Command executed:

  lemur -i example.fastq       --tax-path /home/dbs/lemur_221_db//taxonomy.tsv --num-threads 4 --aln-score AS --rank species --min-aln-len-ratio 0.75 --min-fidelity 0.5 --ref-weight 1.0 --mm2-N 50 --mm2-K 500000000 --mm2-type map-ont             --num-threads 6       --db-prefix lemur_221_db       -o results/
  
  cat <<-END_VERSIONS > versions.yml
  "LEMUR":
      lemur: $(echo $(lemur --version 2>&1) | sed 's/^.*lemur //; s/Using.*$//' )
  END_VERSIONS

Command exit status:
  1

Command output:
  2026-04-29 07:47:03 PM INFO:	Starting run of minimap2 at 2026-04-29 19:47:03.934655
  2026-04-29 07:48:01 PM CRITICAL:	minimap2 failed executing:
  minimap2                             -ax map-ont                             -N 50                             -K 500000000                             -p .9                             -f 0                             --sam-hit-only                             --eqx                             -t 6                             lemur_221_db/species_taxid.fasta                             example.fastq                             -o results//reads.sam
  
  STDOUT:
  
  STDERR:[M::mm_idx_gen::47.511*1.56] collected minimizers
  [M::mm_idx_gen::54.550*2.13] sorted minimizers
  [M::main::54.913*2.12] loaded/built the index for 3335785 target sequence(s)
  [M::mm_mapopt_update::54.913*2.12] mid_occ = 1000000
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 3335785
  [M::mm_idx_stat::55.590*2.10] distinct minimizers: 51995586 (41.46% are singletons); average occurrences: 11.640; average spacing: 5.451; total length: 3299326635
  ERROR: failed to open file 'example.fastq': No such file or directory
  ERROR: failed to map the query file

Command error:
  2026-04-29 07:47:03 PM INFO:	Starting run of minimap2 at 2026-04-29 19:47:03.934655
  2026-04-29 07:48:01 PM CRITICAL:	minimap2 failed executing:
  minimap2                             -ax map-ont                             -N 50                             -K 500000000                             -p .9                             -f 0                             --sam-hit-only                             --eqx                             -t 6                             lemur_221_db/species_taxid.fasta                             example.fastq                             -o results//reads.sam
  
  STDOUT:
  
  STDERR:[M::mm_idx_gen::47.511*1.56] collected minimizers
  [M::mm_idx_gen::54.550*2.13] sorted minimizers
  [M::main::54.913*2.12] loaded/built the index for 3335785 target sequence(s)
  [M::mm_mapopt_update::54.913*2.12] mid_occ = 1000000
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 3335785
  [M::mm_idx_stat::55.590*2.10] distinct minimizers: 51995586 (41.46% are singletons); average occurrences: 11.640; average spacing: 5.451; total length: 3299326635
  ERROR: failed to open file 'example.fastq': No such file or directory
  ERROR: failed to map the query file
  
  2026-04-29 07:48:01 PM CRITICAL:	minimap2 failed executing:
  minimap2                             -ax map-ont                             -N 50                             -K 500000000                             -p .9                             -f 0                             --sam-hit-only                             --eqx                             -t 6                             lemur_221_db/species_taxid.fasta                             example.fastq                             -o results//reads.sam
  
  STDOUT:
  
  STDERR:[M::mm_idx_gen::47.511*1.56] collected minimizers
  [M::mm_idx_gen::54.550*2.13] sorted minimizers
  [M::main::54.913*2.12] loaded/built the index for 3335785 target sequence(s)
  [M::mm_mapopt_update::54.913*2.12] mid_occ = 1000000
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 3335785
  [M::mm_idx_stat::55.590*2.10] distinct minimizers: 51995586 (41.46% are singletons); average occurrences: 11.640; average spacing: 5.451; total length: 3299326635
  ERROR: failed to open file 'example.fastq': No such file or directory
  ERROR: failed to map the query file

Work dir:
  /home/Users/pbk1/somatem/work/96/cd128d8d51da905cbe5c92b33d615b