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Merged
JoseEspinosa merged 10 commits into from
May 12, 2026
Merged

Fix MultiQC file naming and publication #601

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72c43c5
Rename plddt tsv files for multiqc with _mqc.tsv so that they are dis…
JoseEspinosa May 8, 2026
34f8624
Fix publication of multiqc files and centralize it in modules.config
JoseEspinosa May 8, 2026
98ef3ca
Fix multiqc file name
JoseEspinosa May 8, 2026
809d617
Update changelog
JoseEspinosa May 8, 2026
f02a7a8
No need to use prefix multiqc in multiqc filename saveAs
JoseEspinosa May 8, 2026
6e5caf0
Rename "_plddt_mqc.tsv" files to "_plddt.tsv" when published in the c…
JoseEspinosa May 8, 2026
a4dd77e
Make lint happy
JoseEspinosa May 8, 2026
7aa5d86
Update nf-test snapshots
JoseEspinosa May 8, 2026
c4a78f5
Merge branch 'dev' into fixes
JoseEspinosa May 11, 2026
49b7c6d
Make lint happy
JoseEspinosa May 11, 2026
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,9 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [[PR ##573](https://github.com/nf-core/proteinfold/pull/573)] - Adds affiliations for UNSW Structural Biology Facility (SBF).
- [[PR #573](https://github.com/nf-core/proteinfold/pull/573)] - Adds affiliations for UNSW Structural Biology Facility (SBF).
- [[PR #588](https://github.com/nf-core/proteinfold/pulls/588)] - Add `--random_seed` for AF2, Boltz, and ColabFold, removing and replacing `--alphafold2_random_seed`.
- [[PR #597](https://github.com/nf-core/proteinfold/pull/249)] - Update pipeline template to [nf-core/tools 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2).
- [[#598](https://github.com/nf-core/proteinfold/issues/598)] - Remove workflow JSON generation.
- [[#600](https://github.com/nf-core/proteinfold/issues/600)] - Fix multiqc reports publication and centralize the config in `modules.config`.

| Old parameter | New parameter |
| -------------------------- | --------------- |
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2 changes: 1 addition & 1 deletion bin/extract_metrics.py
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Expand Up @@ -128,7 +128,7 @@ def extract_structs_plddt_to_tsv(name, structures):
plddt_rows = [["Positions"] + rank_names]
res_id_col = list(range(len(plddt_cols[0])))
plddt_rows.extend(zip(res_id_col, *plddt_cols)) # Combine lists column-wise to make rows
write_tsv(f"{name}_plddt.tsv", plddt_rows)
write_tsv(f"{name}_plddt_mqc.tsv", plddt_rows)

def read_pkl(name, pkl_files):
"""
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1 change: 1 addition & 0 deletions conf/modules.config
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Expand Up @@ -44,6 +44,7 @@ process {
}

withName: 'MULTIQC' {
ext.prefix = { "${meta.model}" }
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
path: { "${params.outdir}/multiqc" },
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12 changes: 4 additions & 8 deletions conf/modules_alphafold2.config
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Expand Up @@ -22,14 +22,6 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
]
}
withName: 'NFCORE_PROTEINFOLD:POST_PROCESSING:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "alphafold2_$filename" }
]
}

// Configure UNTAR/GUNZIP processes to use correct directory names
withName: '.*ARIA2_ALPHAFOLD2_PARAMS:UNTAR' {
ext.prefix = { "${params.alphafold2_params_prefix}" }
Expand Down Expand Up @@ -104,6 +96,8 @@ process {
saveAs: { filename ->
if(filename.endsWith('_pae.tsv')){
"paes/$filename"
} else if(filename.endsWith('_plddt_mqc.tsv')){
filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv')
} else { filename }
},
pattern: '*.tsv'
Expand Down Expand Up @@ -161,6 +155,8 @@ process {
saveAs: { filename ->
if(filename.endsWith('_pae.tsv')){
"paes/$filename"
} else if(filename.endsWith('_plddt_mqc.tsv')){
filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv')
} else { filename }
},
pattern: '*.tsv'
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10 changes: 2 additions & 8 deletions conf/modules_alphafold3.config
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Expand Up @@ -78,13 +78,6 @@ process {
},
]
}
withName: 'NFCORE_PROTEINFOLD:ALPHAFOLD3:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "alphafold3_$filename" }
]
}
}

//
Expand All @@ -97,7 +90,8 @@ process {
[
path: { "${params.outdir}/alphafold3/${meta.id}" },
mode: 'copy',
pattern: '*_plddt.tsv'
saveAs: { filename -> filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv') },
pattern: '*_plddt_mqc.tsv'
],
[
path: { "${params.outdir}/alphafold3/${meta.id}" },
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12 changes: 2 additions & 10 deletions conf/modules_boltz.config
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Expand Up @@ -79,7 +79,8 @@ process {
[
path: { "${params.outdir}/boltz/${meta.id}" },
mode: 'copy',
pattern: '*_plddt.tsv'
saveAs: { filename -> filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv') },
pattern: '*_plddt_mqc.tsv'
],
[
path: { "${params.outdir}/boltz/${meta.id}" },
Expand Down Expand Up @@ -110,15 +111,6 @@ process {
],
]
}

withName: 'NFCORE_PROTEINFOLD:BOLTZ:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "boltz_$filename" }
]
}

withName: 'BOLTZ_FASTA|MULTIFASTA_TO_CSV|SPLIT_MSA' {
cpus = 1
memory = 2.GB
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10 changes: 2 additions & 8 deletions conf/modules_colabfold.config
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Expand Up @@ -11,14 +11,6 @@
*/

process {
withName: 'NFCORE_PROTEINFOLD:COLABFOLD:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "colabfold_$filename" }
]
}

// Configure UNTAR processes to use correct directory names
withName: '.*ARIA2_COLABFOLD_PARAMS:UNTAR' {
ext.prefix = { "${params.colabfold_params_prefix}" }
Expand Down Expand Up @@ -52,6 +44,8 @@ process {
saveAs: { filename ->
if(filename.endsWith('_pae.tsv')){
"paes/$filename"
} else if(filename.endsWith('_plddt_mqc.tsv')){
filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv')
} else { filename }
},
pattern: '*.tsv'
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12 changes: 2 additions & 10 deletions conf/modules_esmfold.config
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Expand Up @@ -30,7 +30,8 @@ process {
[
path: { "${params.outdir}/esmfold/${meta.id}" },
mode: 'copy',
pattern: '*_plddt.tsv'
saveAs: { filename -> filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv') },
pattern: '*_plddt_mqc.tsv'
],
[
path: { "${params.outdir}/esmfold/top_ranked_structures" },
Expand All @@ -40,13 +41,4 @@ process {
]
]
}

withName: 'NFCORE_PROTEINFOLD:ESMFOLD:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "esmfold_$filename" }
]
}

}
11 changes: 2 additions & 9 deletions conf/modules_helixfold3.config
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Expand Up @@ -111,7 +111,8 @@ process {
[
path: { "${params.outdir}/helixfold3/${meta.id}" },
mode: 'copy',
pattern: '*_plddt.tsv'
saveAs: { filename -> filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv') },
pattern: '*_plddt_mqc.tsv'
],
[
path: { "${params.outdir}/helixfold3/${meta.id}" },
Expand Down Expand Up @@ -155,12 +156,4 @@ process {
]
]
}

withName: 'NFCORE_PROTEINFOLD:HELIXFOLD3:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "helixfold3_$filename" }
]
}
}
11 changes: 2 additions & 9 deletions conf/modules_rosettafold2na.config
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Expand Up @@ -46,7 +46,8 @@ process {
[
path: { "${params.outdir}/rosettafold2na/${meta.id}" },
mode: 'copy',
pattern: '*_plddt.tsv'
saveAs: { filename -> filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv') },
pattern: '*_plddt_mqc.tsv'
],
[
path: { "${params.outdir}/rosettafold2na/${meta.id}" },
Expand Down Expand Up @@ -74,12 +75,4 @@ process {
]
]
}

withName: 'NFCORE_PROTEINFOLD:ROSETTAFOLD2NA:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "rosettafold2na_$filename" }
]
}
}
11 changes: 2 additions & 9 deletions conf/modules_rosettafold_all_atom.config
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Expand Up @@ -25,7 +25,8 @@ process {
[
path: { "${params.outdir}/rosettafold_all_atom/${meta.id}" },
mode: 'copy',
pattern: '*_plddt.tsv'
saveAs: { filename -> filename.replaceAll(/_plddt_mqc\.tsv$/, '_plddt.tsv') },
pattern: '*_plddt_mqc.tsv'
],
[
path: { "${params.outdir}/rosettafold_all_atom/${meta.id}" },
Expand Down Expand Up @@ -54,14 +55,6 @@ process {
]
}

withName: 'NFCORE_PROTEINFOLD:ROSETTAFOLD_ALL_ATOM:MULTIQC' {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : "rosettafold_all_atom_$filename" }
]
}

// Configure UNTAR processes to use correct directory names
withName: '.*PREPARE_ROSETTAFOLD_ALL_ATOM_DBS:ARIA2_WEIGHTS:ARIA2' {
publishDir = [
Expand Down
22 changes: 11 additions & 11 deletions modules/local/colabfold_batch/main.nf
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Expand Up @@ -12,16 +12,16 @@ process COLABFOLD_BATCH {
val numRec

output:
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_colabfold.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("raw/*relaxed_rank_*.pdb") , emit: pdb
tuple val(meta), path ("${meta.id}_colabfold_msa.tsv") , emit: msa
tuple val(meta), path ("${meta.id}_plddt.tsv") , emit: multiqc
tuple val(meta), path ("${meta.id}_*_pae.tsv") , optional: true, emit: paes
tuple val(meta), path ("${meta.id}_0_pae.tsv") , optional: true, emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , optional: true, emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_colabfold.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("raw/*relaxed_rank_*.pdb") , emit: pdb
tuple val(meta), path ("${meta.id}_colabfold_msa.tsv"), emit: msa
tuple val(meta), path ("${meta.id}_plddt_mqc.tsv") , emit: multiqc
tuple val(meta), path ("${meta.id}_*_pae.tsv") , optional: true, emit: paes
tuple val(meta), path ("${meta.id}_0_pae.tsv") , optional: true, emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , optional: true, emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -84,7 +84,7 @@ process COLABFOLD_BATCH {
touch ./raw/${meta.id}_scores_rank.json
touch ./${meta.id}_0_pae.tsv
touch ./${meta.id}_ptm.tsv
touch ./${meta.id}_plddt.tsv
touch ./${meta.id}_plddt_mqc.tsv
touch ./${meta.id}_colabfold_msa.tsv

cat <<-END_VERSIONS > versions.yml
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22 changes: 11 additions & 11 deletions modules/local/run_alphafold2/main.nf
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Expand Up @@ -25,17 +25,17 @@ process RUN_ALPHAFOLD2 {
path ('uniprot/*')

output:
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("raw/ranked*.pdb") , emit: pdb
tuple val(meta), path ("${meta.id}_plddt.tsv") , emit: multiqc
tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv") , emit: msa
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("raw/ranked*.pdb") , emit: pdb
tuple val(meta), path ("${meta.id}_plddt_mqc.tsv") , emit: multiqc
tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv"), emit: msa
// Note: alphafold2_model_preset == "monomer" the pae file won't exist, thus the optional
tuple val(meta), path ("${meta.id}_*_pae.tsv") , optional: true, emit: paes
tuple val(meta), path ("${meta.id}_0_pae.tsv") , optional: true, emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , optional: true, emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions
tuple val(meta), path ("${meta.id}_*_pae.tsv") , optional: true, emit: paes
tuple val(meta), path ("${meta.id}_0_pae.tsv") , optional: true, emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , optional: true, emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -98,7 +98,7 @@ process RUN_ALPHAFOLD2 {
stub:
"""
touch "${meta.id}_alphafold2.pdb"
touch "${meta.id}_plddt.tsv"
touch "${meta.id}_plddt_mqc.tsv"
touch "${meta.id}_alphafold2_msa.tsv"
touch "${meta.id}_0_pae.tsv"
touch "${meta.id}_ptm.tsv"
Expand Down
22 changes: 11 additions & 11 deletions modules/local/run_alphafold2_pred/main.nf
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Expand Up @@ -23,17 +23,17 @@ process RUN_ALPHAFOLD2_PRED {
path ('uniprot/*')

output:
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("raw/ranked*.pdb") , emit: pdb
tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv") , emit: msa
tuple val(meta), path ("${meta.id}_plddt.tsv") , emit: multiqc
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_alphafold2.pdb") , emit: top_ranked_pdb
tuple val(meta), path ("raw/ranked*.pdb") , emit: pdb
tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv"), emit: msa
tuple val(meta), path ("${meta.id}_plddt_mqc.tsv") , emit: multiqc
//Note: alphafold2_model_preset == "monomer" the pae file won't exist.
tuple val(meta), path ("${meta.id}_*_pae.tsv") , optional: true, emit: paes
tuple val(meta), path ("${meta.id}_0_pae.tsv") , optional: true, emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , optional: true, emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions
tuple val(meta), path ("${meta.id}_*_pae.tsv") , optional: true, emit: paes
tuple val(meta), path ("${meta.id}_0_pae.tsv") , optional: true, emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , optional: true, emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -77,7 +77,7 @@ process RUN_ALPHAFOLD2_PRED {
stub:
"""
touch "${meta.id}_alphafold2.pdb"
touch "${meta.id}_plddt.tsv"
touch "${meta.id}_plddt_mqc.tsv"
touch "${meta.id}_alphafold2_msa.tsv"
touch "${meta.id}_0_pae.tsv"
mkdir "raw/"
Expand Down
20 changes: 10 additions & 10 deletions modules/local/run_alphafold3/main.nf
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Expand Up @@ -18,15 +18,15 @@ process RUN_ALPHAFOLD3 {
path "uniprot/*"

output:
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_alphafold3.cif") , emit: top_ranked_cif
tuple val(meta), path ("raw/*ranked_*.cif") , emit: cif
tuple val(meta), path ("${meta.id}_plddt.tsv") , emit: multiqc
tuple val(meta), path ("${meta.id}_alphafold3_msa.tsv") , emit: msa
tuple val(meta), path ("${meta.id}_0_pae.tsv") , emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions
path ("raw/**") , emit: raw
tuple val(meta), path ("${meta.id}_alphafold3.cif") , emit: top_ranked_cif
tuple val(meta), path ("raw/*ranked_*.cif") , emit: cif
tuple val(meta), path ("${meta.id}_plddt_mqc.tsv") , emit: multiqc
tuple val(meta), path ("${meta.id}_alphafold3_msa.tsv"), emit: msa
tuple val(meta), path ("${meta.id}_0_pae.tsv") , emit: pae
tuple val(meta), path ("${meta.id}_ptm.tsv") , emit: ptms
tuple val(meta), path ("${meta.id}_iptm.tsv") , optional: true, emit: iptms
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -129,7 +129,7 @@ process RUN_ALPHAFOLD3 {
touch raw/${prefix}_ranked_3.cif
touch raw/${prefix}_ranked_4.cif
touch raw/${prefix}_ranked_5.cif
touch ${prefix}_plddt.tsv
touch ${prefix}_plddt_mqc.tsv
touch ${prefix}_alphafold3_msa.tsv
touch ${prefix}_0_pae.tsv
touch ${prefix}_ptm.tsv
Expand Down
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