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main_metamorpheus.nf
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main_metamorpheus.nf
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// Channel
// .value(file(params.toml))
// .ifEmpty { error "Cannot find toml file for parameter --toml: ${params.toml}" }
// .set { ch_toml }
// Channel
// .value(file(params.orf_calls))
// .ifEmpty { error "Cannot find gtf file for parameter --gencode_gtf: ${params.orf_calls}" }
// .set { ch_orf_calls }
// TODO - is orf_fasta the refined database? If so, can we call this parameter --refined_protein_db or somethign like that?
// TODO cont. - orf typically means the nt sequence underlying the protein
if (!params.sqanti_fasta) exit 1, "Cannot find any sqanti_fasta file for parameter --sqanti_fasta: ${params.sqanti_fasta}"
ch_orf_fasta = Channel.value(file(params.sqanti_fasta))
if (!params.orf_meta) exit 1, "Cannot find any sqanti_fasta file for parameter --orf_meta: ${params.orf_meta}"
ch_orf_meta = Channel.value(file(params.orf_meta))
Channel
.fromPath("${params.mass_spec}/*.raw")
.set{ch_mass_spec_raw}
Channel
.fromPath("${params.mass_spec}/*.{mzml,mzML}")
.set{ch_mass_spec_mzml}
if (!params.rescue_resolve_toml) exit 1, "Cannot find file for parameter --rescue_resolve_toml: ${params.rescue_resolve_toml}"
ch_rr_toml = Channel.value(file(params.rescue_resolve_toml))
ch_metamorpheus_toml = Channel.value(file(params.metamorpheus_toml))
process mass_spec_raw_convert{
publishDir "${params.outdir}/raw_convert/", mode: 'copy'
input:
file(raw_file) from ch_mass_spec_raw
output:
file("*") into ch_mass_spec_converted
script:
"""
wine msconvert $raw_file --filter "peakPicking true 1-"
"""
}
// TODO - can you explain to me why this was needed?
ch_mass_spec_combined = ch_mass_spec_mzml.concat(ch_mass_spec_converted)
ch_mass_spec_combined.into{
ch_mass_spec_for_pacbio_rescue_resolve
ch_mass_spec_for_pacbio_normal
}
process metamorpheus_with_sample_specific_database{
tag " $mass_spec"
label 'metamorpheus'
publishDir "${params.outdir}/metamorpheus/", mode: 'copy'
input:
// file(orf_calls) from ch_orf_calls
file(orf_fasta) from ch_orf_fasta
file(toml_file) from ch_metamorpheus_toml
file(mass_spec) from ch_mass_spec_for_pacbio_normal.collect()
output:
file("*")
script:
def toml = toml_file.name != 'NO_TOML_FILE' ? "$toml_file" : 'toml/SearchTask.toml'
"""
echo $toml > toml_given.txt
echo $toml_file > toml_used.txt
dotnet /metamorpheus/CMD.dll -g -o ./toml --mmsettings settings
dotnet /metamorpheus/CMD.dll -d $orf_fasta -s $mass_spec -t $toml -v normal --mmsettings settings -o ./search_results
"""
}
// process metamorpheus_with_sample_specific_database_rescue_resolve{
// tag " $mass_spec"
// publishDir "${params.outdir}/metamorpheus/rescue_resolve", mode: 'copy'
// input:
// // file(orf_calls) from ch_orf_calls
// file(orf_fasta) from ch_orf_fasta
// // file(toml) from ch_toml
// file(mass_spec) from ch_mass_spec_for_pacbio_rescue_resolve.collect()
// file(toml) from ch_rr_toml
// file(orf_meta) from ch_orf_meta
// output:
// file("toml/*")
// file("search_results/Task1SearchTask/All*")
// file("search_results/Task1SearchTask/prose.txt")
// file("search_results/Task1SearchTask/results.txt")
// file("search_results/Task1SearchTask/AllPeptides.${params.name}.rescue_resolve.psmtsv")
// file("search_results/Task1SearchTask/AllQuantifiedProteinGroups.${params.name}.rescue_resolve.tsv")
// script:
// """
// dotnet /metamorpheus/CMD.dll -g -o ./toml --mmsettings settings
// dotnet /metamorpheus/CMD.dll -d $orf_fasta -s $mass_spec -t $toml -v normal --mmsettings settings -o ./search_results --orf $orf_meta --cpm 25
// mv search_results/Task1SearchTask/AllPeptides.psmtsv search_results/Task1SearchTask/AllPeptides.${params.name}.rescue_resolve.psmtsv
// mv search_results/Task1SearchTask/AllQuantifiedProteinGroups.tsv search_results/Task1SearchTask/AllQuantifiedProteinGroups.${params.name}.rescue_resolve.tsv
// """
// }
// process metamorpheus_with_gencode_database{
// tag " $mass_spec"
// publishDir "${params.outdir}/metamorpheus/", mode: 'copy'
// input:
// // file(orf_calls) from ch_orf_calls
// TODO - is the below variable specific enough? e.g., ch_gencode_translations_fasta
// file(gencode_fasta) from ch_gencode_fasta
// // file(toml) from ch_toml
// file(mass_spec) from ch_mass_spec_combined.collect()
// output:
// file("*")
// file("AllPeptides.psmtsv") into ch_gencode_peptides
// script:
// """
// dotnet /metamorpheus/CMD.dll -g -o ./ --mmsettings settings
// dotnet /metamorpheus/CMD.dll -d $gencode_fasta -s $mass_spec -t SearchTask.toml -v normal --mmsettings settings
// """
// }