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update main from dev. #4

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Merged
ziadbkh merged 2 commits into from
Jul 14, 2026
Merged

update main from dev. #4

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db63298
minor fix for monomer input
ziadbkh Jul 6, 2026
2e44f01
accept ptm when no iptm
ziadbkh Jul 14, 2026
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13 changes: 7 additions & 6 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ workflow WF_WISPS {
params.pool,
params.pool_size
)
ch_versions = ch_versions.mix(WISPS.out.versions)
ch_versions = ch_versions.mix(WISPS.out.versions)

emit:
multiqc_report = WISPS.out.multiqc_report
Expand All @@ -90,9 +90,10 @@ workflow WF_WISPS {
msa_json = WISPS.out.msa_json.map{['json': it[1]]}
msa_yaml = WISPS.out.msa_yaml.map{['yaml': it[1]]}
msa_csv = WISPS.out.msa_csv.map{['csv': it[1]]}

colabfold_predictions = WISPS.out.colabfold_scores
.join(WISPS.out.colabfold_pdb)
.map { ['score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).iptm : null,
.map { ['score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).with { (iptm && iptm != 0) ? iptm : ptm } : null,
'pdb': it[2],
'confidence': it[1]] }
.filter{params.iptm_threshold == 0 || it.score >= params.iptm_threshold}
Expand All @@ -103,14 +104,14 @@ workflow WF_WISPS {
.map { ['confidence': it[3],
'cif': it[2],
'pae': it[1],
'score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[3].text).iptm : null] }
'score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[3].text).with { (iptm && iptm != 0) ? iptm : ptm } : null] }
.filter{params.iptm_threshold == 0 || it.score >= params.iptm_threshold}

af3_predictions = WISPS.out.alphafold3_confidence
.join(WISPS.out.alphafold3_cif)
.map { ['confidence': it[1],
'cif': it[2],
'score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).iptm : null] }
'score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).with { (iptm && iptm != 0) ? iptm : ptm } : null] }
.filter{params.iptm_threshold == 0 || it.score >= params.iptm_threshold}
}
/*
Expand Down Expand Up @@ -149,7 +150,6 @@ workflow {
params.hook_url,
WF_WISPS.out.multiqc_report
)

publish:
colabfold_predictions = WF_WISPS.out.colabfold_predictions
boltz_predictions = WF_WISPS.out.boltz_predictions
Expand All @@ -161,7 +161,7 @@ workflow {
msa_json = WF_WISPS.out.msa_json.ifEmpty([])
msa_yaml = WF_WISPS.out.msa_yaml.ifEmpty([])
msa_csv = WF_WISPS.out.msa_csv.ifEmpty([])

}

output {
Expand Down Expand Up @@ -212,6 +212,7 @@ output {

}


/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
Expand Down
17 changes: 11 additions & 6 deletions workflows/wisps.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ workflow WISPS {
main:
ch_multiqc_files = Channel.empty()
ch_confidence_scores = Channel.empty()

use_interaction_pools = (pool instanceof Boolean) ? pool : pool.toString().toBoolean()
interaction_mode = mode.split(",").collect { pair ->
pair.split('-').sort().join('-')
Expand Down Expand Up @@ -223,12 +223,12 @@ workflow WISPS {
ch_interaction_raw = ch_samplesheet
.map { it[1] }
.filter { it.extension == "fasta" || it.extension == "fa" }
.ifEmpty { error("Manual mode requires at least one FASTA file in the samplesheet sequence column.") }
.ifEmpty { error("Manual mode requires at least one FASTA file in the samplesheet sequence column-Z.") }
.collectFile(name: "manual_interactions.fasta", newLine: false) { fasta_file ->
["manual_interactions.fasta", fasta_file.text.trim() + "\n"]
}
}

ch_interaction_has_protein = ch_interaction_raw.flatMap { interactions_fasta ->
def out = []
def lines = interactions_fasta.readLines().findAll { it?.trim() }
Expand Down Expand Up @@ -581,6 +581,7 @@ workflow WISPS {
.map { [it[0].id, it[0]] }
.groupTuple()
.map { inputId, metas -> [inputId, metas] }


ch_long = Channel.empty()
if ('boltz' in active_modes)
Expand All @@ -589,8 +590,9 @@ workflow WISPS {
ch_long = ch_long.mix(ch_ipsae_out.colabfold.flatMap { id, entries -> entries.collect { e -> [id, e[0], 'colabfold', e[1]] } })
if ('alphafold3' in active_modes)
ch_long = ch_long.mix(ch_ipsae_out.alphafold3.flatMap { id, entries -> entries.collect { e -> [id, e[0], 'alphafold3', e[1]] } })

ch_long = ch_long
.join(ch_report_meta_grouped_by_input_id, remainder: true)
.join(ch_report_meta_grouped_by_input_id, remainder: false)
.flatMap { inputId, pairId, model, score, metaList ->
def metas = (metaList instanceof List && !metaList.isEmpty())
? metaList
Expand All @@ -600,7 +602,8 @@ workflow WISPS {
[reportId, pairId, model, score]
}
}



// 2) Pivot per pair: [pair_id, sampleModelScoreMap]
ch_pair_wide = ch_long
.map { sampleId, pairId, model, score -> [pairId, [sampleId, model, score]] }
Expand All @@ -612,7 +615,9 @@ workflow WISPS {
}
[pairId, bySample]
}



//ch_pair_wide.view()
// 3) Create one CSV per pair with model-only headers
ch_interaction_in.map { it[0].report_id }.unique().toSortedList().map { [sample_ids: it] }
.combine(ch_pair_wide.collect(flat: false).map { [pairs: it] })
Expand Down
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