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nf_workflow.nf
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nf_workflow.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
params.usi_field = "mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00005436077"
// Search Type
params.entrymode = "file"
params.usi_file = "usi_to_search.tsv"
// Parameters
params.database = "gnpsdata_index"
params.analog = "No"
params.precursor_tolerance = "0.02"
params.fragment_tolerance = "0.02"
params.cosine = "0.7"
TOOL_FOLDER = "$baseDir/bin"
// Boilerplate for GNPS2
params.OMETAPARAM_YAML = "job_parameters.yaml"
params.input_gnps2_parameters = params.OMETAPARAM_YAML
process prepData {
publishDir "./nf_output", mode: 'copy'
conda "$TOOL_FOLDER/conda_env.yml"
input:
file input_parameters
output:
file 'usi_to_search.tsv'
"""
python $TOOL_FOLDER/prep_input.py $input_parameters usi_to_search.tsv
"""
}
process searchFASST {
publishDir "./nf_output", mode: 'copy'
conda "$TOOL_FOLDER/conda_env.yml"
input:
file input
output:
file 'output.tsv'
"""
python $TOOL_FOLDER/masst_client.py $input output.tsv \
--analog ${params.analog} \
--precursor_tolerance ${params.precursor_tolerance} \
--fragment_tolerance ${params.fragment_tolerance} \
--cosine ${params.cosine} \
--database ${params.database}
"""
}
workflow {
input_parameters_ch = Channel.fromPath(params.input_gnps2_parameters)
if(params.entrymode == "file"){
usi_to_search_ch = Channel.fromPath(params.usi_file)
}
else{
usi_to_search_ch = prepData(input_parameters_ch)
}
searchFASST(usi_to_search_ch)
}