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keiran-rowell-unswkeiran-rowell-unsw
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remove hard to read inconsistent whitespace in channel construction
1 parent 3570829 commit 77af3e3

1 file changed

Lines changed: 46 additions & 42 deletions

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‎main.nf‎

Lines changed: 46 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -136,10 +136,11 @@ workflow NFCORE_PROTEINFOLD {
136136
PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
137137
PREPARE_ALPHAFOLD2_DBS.out.uniprot
138138
)
139-
ch_multiqc = ch_multiqc.mix(ALPHAFOLD2.out.multiqc_report.collect())
140-
ch_versions = ch_versions.mix(ALPHAFOLD2.out.versions)
141-
ch_report_input = ch_report_input
142-
.mix(ALPHAFOLD2.out.pdb
139+
ch_multiqc = ch_multiqc.mix(ALPHAFOLD2.out.multiqc_report.collect())
140+
ch_versions = ch_versions.mix(ALPHAFOLD2.out.versions)
141+
ch_report_input = ch_report_input
142+
.mix(
143+
ALPHAFOLD2.out.pdb
143144
.join(ALPHAFOLD2.out.msa)
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.join(ALPHAFOLD2.out.pae)
145146
)
@@ -241,8 +242,9 @@ workflow NFCORE_PROTEINFOLD {
241242

242243
ch_multiqc = ch_multiqc.mix(COLABFOLD.out.multiqc_report)
243244
ch_versions = ch_versions.mix(COLABFOLD.out.versions)
244-
ch_report_input = ch_report_input
245-
.mix(COLABFOLD.out.pdb
245+
ch_report_input = ch_report_input
246+
.mix(
247+
COLABFOLD.out.pdb
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.join(COLABFOLD.out.msa)
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.join(COLABFOLD.out.pae)
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)
@@ -279,11 +281,12 @@ workflow NFCORE_PROTEINFOLD {
279281

280282
ch_multiqc = ch_multiqc.mix(ESMFOLD.out.multiqc_report.collect())
281283
ch_versions = ch_versions.mix(ESMFOLD.out.versions)
282-
ch_report_input = ch_report_input.mix(
283-
ESMFOLD.out.pdb
284-
.combine(ch_dummy_msa)
285-
.combine(ch_dummy_pae)
286-
)
284+
ch_report_input = ch_report_input
285+
.mix(
286+
ESMFOLD.out.pdb.map { meta, pdb -> [meta, [pdb]] }
287+
.combine(ch_dummy_msa)
288+
.combine(ch_dummy_pae)
289+
)
287290
ch_top_ranked_model = ch_top_ranked_model.mix(ESMFOLD.out.pdb)
288291
}
289292

@@ -321,13 +324,15 @@ workflow NFCORE_PROTEINFOLD {
321324
PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.pdb100,
322325
PREPARE_ROSETTAFOLD_ALL_ATOM_DBS.out.rfaa_paper_weights
323326
)
324-
ch_multiqc = ch_multiqc.mix(ROSETTAFOLD_ALL_ATOM.out.multiqc_report.collect())
325-
ch_versions = ch_versions.mix(ROSETTAFOLD_ALL_ATOM.out.versions)
326-
ch_report_input = ch_report_input.mix(ROSETTAFOLD_ALL_ATOM.out.pdb
327-
.join(ROSETTAFOLD_ALL_ATOM.out.msa)
328-
.join(ROSETTAFOLD_ALL_ATOM.out.pae)
329-
)
330-
ch_top_ranked_model = ch_top_ranked_model.mix(ROSETTAFOLD_ALL_ATOM.out.pdb)
327+
ch_multiqc = ch_multiqc.mix(ROSETTAFOLD_ALL_ATOM.out.multiqc_report.collect())
328+
ch_versions = ch_versions.mix(ROSETTAFOLD_ALL_ATOM.out.versions)
329+
ch_report_input = ch_report_input
330+
.mix(
331+
ROSETTAFOLD_ALL_ATOM.out.pdb.map { meta, pdb -> [meta, [pdb]] }
332+
.join(ROSETTAFOLD_ALL_ATOM.out.msa)
333+
.join(ROSETTAFOLD_ALL_ATOM.out.pae)
334+
)
335+
ch_top_ranked_model = ch_top_ranked_model.mix(ROSETTAFOLD_ALL_ATOM.out.pdb)
331336
}
332337

333338
//
@@ -391,10 +396,11 @@ workflow NFCORE_PROTEINFOLD {
391396
PREPARE_HELIXFOLD3_DBS.out.helixfold3_init_models,
392397
PREPARE_HELIXFOLD3_DBS.out.helixfold3_maxit_src
393398
)
394-
ch_multiqc = ch_multiqc.mix(HELIXFOLD3.out.multiqc_report.collect())
395-
ch_versions = ch_versions.mix(HELIXFOLD3.out.versions)
396-
ch_report_input = ch_report_input
397-
.mix(HELIXFOLD3.out.pdb
399+
ch_multiqc = ch_multiqc.mix(HELIXFOLD3.out.multiqc_report.collect())
400+
ch_versions = ch_versions.mix(HELIXFOLD3.out.versions)
401+
ch_report_input = ch_report_input
402+
.mix(
403+
HELIXFOLD3.out.pdb
398404
.join(HELIXFOLD3.out.msa)
399405
.join(HELIXFOLD3.out.pae)
400406
)
@@ -440,18 +446,15 @@ workflow NFCORE_PROTEINFOLD {
440446
PREPARE_ROSETTAFOLD2NA_DBS.out.rna,
441447
PREPARE_ROSETTAFOLD2NA_DBS.out.rosettafold2na_weights
442448
)
443-
ch_multiqc = ch_multiqc.mix(ROSETTAFOLD2NA.out.multiqc_report.collect())
444-
ch_versions = ch_versions.mix(ROSETTAFOLD2NA.out.versions)
445-
ch_report_input = ch_report_input
446-
.mix(
447-
ROSETTAFOLD2NA
448-
.out
449-
.pdb
450-
.map { meta, pdb -> [ meta, [ pdb ] ] }
451-
.join(ROSETTAFOLD2NA.out.msa)
452-
.join(ROSETTAFOLD2NA.out.pae)
453-
)
454-
ch_top_ranked_model = ch_top_ranked_model.mix(ROSETTAFOLD2NA.out.pdb)
449+
ch_multiqc = ch_multiqc.mix(ROSETTAFOLD2NA.out.multiqc_report.collect())
450+
ch_versions = ch_versions.mix(ROSETTAFOLD2NA.out.versions)
451+
ch_report_input = ch_report_input
452+
.mix(
453+
ROSETTAFOLD2NA.out.pdb.map { meta, pdb -> [meta, [pdb]] }
454+
.join(ROSETTAFOLD2NA.out.msa)
455+
.join(ROSETTAFOLD2NA.out.pae)
456+
)
457+
ch_top_ranked_model = ch_top_ranked_model.mix(ROSETTAFOLD2NA.out.pdb)
455458
}
456459

457460
// WORKFLOW: Run Boltz
@@ -498,14 +501,15 @@ workflow NFCORE_PROTEINFOLD {
498501
PREPARE_COLABFOLD_DBS_BOLTZ.out.uniref30,
499502
params.use_msa_server
500503
)
501-
ch_multiqc = ch_multiqc.mix(BOLTZ.out.multiqc_report)
502-
ch_versions = ch_versions.mix(BOLTZ.out.versions)
503-
ch_report_input = ch_report_input.mix(
504-
BOLTZ.out.pdb
505-
.join(BOLTZ.out.msa)
506-
.join(BOLTZ.out.pae)
507-
)
508-
ch_top_ranked_model = ch_top_ranked_model.mix(BOLTZ.out.top_ranked_pdb)
504+
ch_multiqc = ch_multiqc.mix(BOLTZ.out.multiqc_report)
505+
ch_versions = ch_versions.mix(BOLTZ.out.versions)
506+
ch_report_input = ch_report_input
507+
.mix(
508+
BOLTZ.out.pdb
509+
.join(BOLTZ.out.msa)
510+
.join(BOLTZ.out.pae)
511+
)
512+
ch_top_ranked_model = ch_top_ranked_model.mix(BOLTZ.out.top_ranked_pdb)
509513
}
510514
//
511515
// POST PROCESSING: generate visualisation reports

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