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library creation #341

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merged 2 commits into from
Jan 13, 2024
Merged

library creation #341

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3c80318
Merge pull request #12 from TalusBio/bb_feature/skip_prelim
daichengxin Jan 10, 2024
666467d
library creation
daichengxin Jan 13, 2024
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11 changes: 7 additions & 4 deletions nextflow.config
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Expand Up @@ -174,10 +174,13 @@ params {
species_genes = false
diann_normalize = true
diann_speclib = null

/// DIA-NN: Extras
skip_preliminary_analysis = false
empirical_assembly_log = null

// DIA-NN: Extras
skip_preliminary_analysis = false
empirical_assembly_log = null
random_preanalysis = false
empirical_assembly_ms_n = 200


// MSstats general options
msstats_remove_one_feat_prot = true
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13 changes: 13 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -967,6 +967,19 @@
"description": "Enable cross-run normalization between runs by diann.",
"default": true,
"fa_icon": "far fa-check-square"
},
"random_preanalysis": {
"type": "boolean",
"description": "Enable random selection of spectrum files to generate empirical library.",
"default": false,
"fa_icon": "far fa-check-square"
},
"empirical_assembly_ms_n": {
"type": "integer",
"description": "The number of randomly selected spectrum files.",
"default": 200,
"fa_icon": "fas fa-filter",
"hidden": true
}
},
"fa_icon": "fas fa-braille"
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6 changes: 5 additions & 1 deletion workflows/dia.nf
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Expand Up @@ -75,7 +75,11 @@ workflow DIA {
//
// MODULE: DIANN_PRELIMINARY_ANALYSIS
//
DIANN_PRELIMINARY_ANALYSIS(ch_file_preparation_results.combine(speclib))
if (params.random_preanalysis){
DIANN_PRELIMINARY_ANALYSIS(ch_file_preparation_results.randomSample(params.empirical_assembly_ms_n, 2024).combine(speclib))
} else{
DIANN_PRELIMINARY_ANALYSIS(ch_file_preparation_results.combine(speclib))
}
ch_software_versions = ch_software_versions
.mix(DIANN_PRELIMINARY_ANALYSIS.out.version.ifEmpty(null))

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