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Moving post-processing logic to a subworkflow #210

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merged 6 commits into from
Nov 4, 2024
Merged

Moving post-processing logic to a subworkflow #210

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9c11460
moving into sub-workflow
Oct 30, 2024
13bbbf6
make lint happy and patch multiqc
Oct 30, 2024
dcaede7
make lint happy
Oct 30, 2024
da6b9c0
Merge branch 'dev' into postprocessing-sub-workflow
JoseEspinosa Oct 30, 2024
0abae00
Make prettier happy
JoseEspinosa Oct 30, 2024
92ac346
Fix minimun nxf version in config
JoseEspinosa Oct 30, 2024
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129 changes: 54 additions & 75 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -32,10 +32,7 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nf
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
include { getColabfoldAlphafold2Params } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
include { getColabfoldAlphafold2ParamsPath } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'

include { GENERATE_REPORT } from './modules/local/generate_report'
include { COMPARE_STRUCTURES } from './modules/local/compare_structures'
include { FOLDSEEK_EASYSEARCH } from './modules/nf-core/foldseek/easysearch/main'
include { POST_PROCESSING } from './subworkflows/local/post_processing'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -61,11 +58,15 @@ workflow NFCORE_PROTEINFOLD {
samplesheet // channel: samplesheet read in from --input

main:
ch_samplesheet = samplesheet
ch_multiqc = Channel.empty()
ch_versions = Channel.empty()
ch_report_input = Channel.empty()
requested_modes = params.mode.toLowerCase().split(",")
ch_samplesheet = samplesheet
ch_multiqc = Channel.empty()
ch_versions = Channel.empty()
ch_report_input = Channel.empty()
ch_foldseek_db = Channel.empty()
ch_colabfold_out = Channel.empty()
ch_esmfold_out = Channel.empty()
ch_alphafold2_out = Channel.empty()
requested_modes = params.mode.toLowerCase().split(",")
//
// WORKFLOW: Run alphafold2
//
Expand Down Expand Up @@ -121,11 +122,16 @@ workflow NFCORE_PROTEINFOLD {
PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
PREPARE_ALPHAFOLD2_DBS.out.uniprot
)
ch_multiqc = ALPHAFOLD2.out.multiqc_report
ch_multiqc = ch_multiqc.mix(ALPHAFOLD2.out.multiqc_report.collect())
ch_versions = ch_versions.mix(ALPHAFOLD2.out.versions)
ch_report_input = ch_report_input.mix(
ALPHAFOLD2.out.pdb.join(ALPHAFOLD2.out.msa).map{it[0]["model"] = "alphafold2"; it}
)
ALPHAFOLD2
.out
.main_pdb
.map{[it[0]["id"], it[0], it[1]]}
.set{ch_alphafold2_out}
}

//
Expand Down Expand Up @@ -160,7 +166,7 @@ workflow NFCORE_PROTEINFOLD {
PREPARE_COLABFOLD_DBS.out.uniref30,
params.num_recycles_colabfold
)
ch_multiqc = COLABFOLD.out.multiqc_report
ch_multiqc = ch_multiqc.mix(COLABFOLD.out.multiqc_report)
ch_versions = ch_versions.mix(COLABFOLD.out.versions)
ch_report_input = ch_report_input.mix(
COLABFOLD
Expand All @@ -169,6 +175,14 @@ workflow NFCORE_PROTEINFOLD {
.join(COLABFOLD.out.msa)
.map { it[0]["model"] = "colabfold"; it }
)
COLABFOLD
.out
.main_pdb
.map{[it[0]["id"], it[0], it[1]]}
.join(COLABFOLD.out.msa
.map{[it[0]["id"], it[1]]},
remainder:true
).set{ch_colabfold_out}
}

//
Expand Down Expand Up @@ -196,84 +210,49 @@ workflow NFCORE_PROTEINFOLD {
PREPARE_ESMFOLD_DBS.out.params,
params.num_recycles_esmfold
)
ch_multiqc = ESMFOLD.out.multiqc_report
ch_multiqc = ch_multiqc.mix(ESMFOLD.out.multiqc_report.collect())
ch_versions = ch_versions.mix(ESMFOLD.out.versions)
ch_report_input = ch_report_input.mix(
ESMFOLD.out.pdb.combine(Channel.fromPath("$projectDir/assets/NO_FILE")).map{it[0]["model"] = "esmfold"; it}
)
ch_report_input.filter{it[0]["model"] == "esmfold"}
.map{[it[0]["id"], it[0], it[1], it[2]]}
.set{ch_esmfold_out}
}
//
// POST PROCESSING: generate visulaisation reports
//
if (!params.skip_visualisation){
GENERATE_REPORT(
ch_report_input.map{[it[0], it[1]]},
ch_report_input.map{[it[0], it[2]]},
ch_report_input.map{it[0].model},
Channel.fromPath("$projectDir/assets/proteinfold_template.html", checkIfExists: true).first()
)
ch_versions = ch_versions.mix(GENERATE_REPORT.out.versions)
//GENERATE_REPORT.out.sequence_coverage.view()
if (requested_modes.size() > 1){
ch_report_input.filter{it[0]["model"] == "esmfold"}
.map{[it[0]["id"], it[0], it[1], it[2]]}
.set{ch_comparision_report_files}

if (requested_modes.contains("alphafold2")) {
ch_comparision_report_files = ch_comparision_report_files.mix(
ALPHAFOLD2
.out
.main_pdb
.map{[it[0]["id"], it[0], it[1]]}
.join(GENERATE_REPORT.out.sequence_coverage
.filter{it[0]["model"] == "alphafold2"}
.map{[it[0]["id"], it[1]]}, remainder:true
)
)
}
if (requested_modes.contains("colabfold")) {
ch_comparision_report_files = ch_comparision_report_files.mix(
COLABFOLD
.out
.main_pdb
.map{[it[0]["id"], it[0], it[1]]}
.join(COLABFOLD.out.msa
.map{[it[0]["id"], it[1]]},
remainder:true
)
)
}

ch_comparision_report_files
.groupTuple(by: [0], size: requested_modes.size())
.set{ch_comparision_report_input}

COMPARE_STRUCTURES(
ch_comparision_report_input.map{it[1][0]["models"] = params.mode.toLowerCase(); [it[1][0], it[2]]},
ch_comparision_report_input.map{it[1][0]["models"] = params.mode.toLowerCase(); [it[1][0], it[3]]},
Channel.fromPath("$projectDir/assets/comparison_template.html", checkIfExists: true).first()
)
ch_versions = ch_versions.mix(COMPARE_STRUCTURES.out.versions)
}
}

if (params.foldseek_search == "easysearch"){
ch_foldseek_db = channel.value([["id": params.foldseek_db],
file(params.foldseek_db_path,
checkIfExists: true)])

FOLDSEEK_EASYSEARCH(
ch_report_input
.map{
if (it[0].model == "esmfold")
[it[0], it[1]]
else
[it[0], it[1][0]]
},
ch_foldseek_db
)
}

ch_multiqc_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo ) : Channel.empty()
ch_multiqc_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
//ch_multiqc.view()
POST_PROCESSING(
params.skip_visualisation,
requested_modes.size(),
ch_report_input,
Channel.fromPath("$projectDir/assets/proteinfold_template.html", checkIfExists: true).first(),
Channel.fromPath("$projectDir/assets/comparison_template.html", checkIfExists: true).first(),
params.foldseek_search,
ch_foldseek_db,
params.skip_multiqc,
params.outdir,
ch_versions,
ch_multiqc,
Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true).first(),
ch_multiqc_config.first(),
ch_multiqc_logo.first(),
ch_multiqc_methods_description.first(),
ch_alphafold2_out,
ch_esmfold_out,
ch_colabfold_out
)

emit:
multiqc_report = ch_multiqc
}
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/multiqc/main.nf
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