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Merged
ypriverol merged 4 commits into from
Jul 11, 2026
Merged

update openms and rescoring #712

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bfda029
Merge pull request #91 from bigbio/dev
daichengxin Jun 24, 2026
4527d64
Merge pull request #92 from bigbio/dev
daichengxin Jul 10, 2026
87b5dec
update openms and rescoring
daichengxin Jul 10, 2026
5609d6d
update
daichengxin Jul 10, 2026
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -33,4 +33,4 @@ template:
name: quantms
org: bigbio
outdir: .
version: 1.8.0
version: 1.9.0dev
2 changes: 1 addition & 1 deletion conf/dev.config
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Expand Up @@ -19,7 +19,7 @@ params {
process {
withLabel: openms {
// Conda is no longer supported
container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !task.ext.singularity_pull_docker_container ? 'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' : 'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"}
container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !task.ext.singularity_pull_docker_container ? 'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' : 'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"}
}

// ONSITE uses its own container (not OpenMS thirdparty)
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2 changes: 1 addition & 1 deletion conf/modules/shared.config
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Expand Up @@ -34,7 +34,7 @@ process {
}

// Result tables from multiple pipelines including LFQ, TMT, DDA
withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|ISOBARIC_WORKFLOW' {
withName: '.*:PROTEOMICSLFQ|MSSTATS_CONVERTER|ISOBARIC_WORKFLOW' {
publishDir = [
path: { "${params.outdir}/quant_tables" },
mode: 'copy',
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48 changes: 0 additions & 48 deletions conf/modules/verbose_modules.config
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Expand Up @@ -19,14 +19,6 @@ process {
]
}

withName: '.*:ISOBARIC_ANALYZER' {
publishDir = [
path: { "${params.outdir}/spectra/isobaric_analyzer" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:(MZML_INDEXING|SPECTRUM_FEATURES|MZML_STATISTICS)' {
publishDir = [
path: { "${params.outdir}/spectra/${task.process.tokenize(':')[-1].toLowerCase()}" },
Expand Down Expand Up @@ -68,46 +60,6 @@ process {
]
}

withName: '.*:EXTRACT_PSM_FEATURES' {
publishDir = [
path: { "${params.outdir}/peptide_postprocessing/psm_features" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:CONSENSUSID' {
publishDir = [
path: { "${params.outdir}/peptide_postprocessing/consensusid" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*.FDR_CONSENSUSID:*' {
publishDir = [
path: { "${params.outdir}/peptide_postprocessing/fdr_consensusid" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:ID_FILTER' {
publishDir = [
path: { "${params.outdir}/peptide_postprocessing/id_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:FALSE_DISCOVERY_RATE' {
publishDir = [
path: { "${params.outdir}/peptide_postprocessing/false_discovery_rate" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:MSRESCORE_FEATURES' {
publishDir = [
path: { "${params.outdir}/peptide_postprocessing/msrescore_features" },
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4 changes: 2 additions & 2 deletions modules/local/openms/comet/main.nf
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Expand Up @@ -4,8 +4,8 @@ process COMET {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
tuple val(meta), path(mzml_file), path(database)
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37 changes: 0 additions & 37 deletions modules/local/openms/file_merge/main.nf
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33 changes: 0 additions & 33 deletions modules/local/openms/file_merge/meta.yml
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4 changes: 2 additions & 2 deletions modules/local/openms/generate_decoy_database/main.nf
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Expand Up @@ -3,8 +3,8 @@ process GENERATE_DECOY_DATABASE {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
path(db_for_decoy)
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36 changes: 0 additions & 36 deletions modules/local/openms/id_merger/main.nf
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33 changes: 0 additions & 33 deletions modules/local/openms/id_merger/meta.yml
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4 changes: 2 additions & 2 deletions modules/local/openms/isobaric_workflow/main.nf
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Expand Up @@ -4,8 +4,8 @@ process ISOBARIC_WORKFLOW {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
val(labelling_type)
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4 changes: 2 additions & 2 deletions modules/local/openms/msgf/main.nf
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Expand Up @@ -4,8 +4,8 @@ process MSGF {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
tuple val(meta), path(mzml_file), path(database), path(cnlcp), path(canno), path(csarr), path(cseq)
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4 changes: 2 additions & 2 deletions modules/local/openms/msstats_converter/main.nf
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Expand Up @@ -4,8 +4,8 @@ process MSSTATS_CONVERTER {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
path consensusXML
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4 changes: 2 additions & 2 deletions modules/local/openms/mzml_indexing/main.nf
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Expand Up @@ -4,8 +4,8 @@ process MZML_INDEXING {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
tuple val(meta), path(mzmlfile)
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4 changes: 2 additions & 2 deletions modules/local/openms/openms_peak_picker/main.nf
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Expand Up @@ -4,8 +4,8 @@ process OPENMS_PEAK_PICKER {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
tuple val(meta), path(mzml_file)
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6 changes: 4 additions & 2 deletions modules/local/openms/percolator/main.nf
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Expand Up @@ -4,8 +4,8 @@ process PERCOLATOR {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
tuple val(meta), path(id_file)
Expand All @@ -18,6 +18,7 @@ process PERCOLATOR {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.mzml_id}"
def best_per_spectrum_only = params.best_per_spectrum_only ? "-best_per_spectrum_only" : ""

"""
OMP_NUM_THREADS=$task.cpus PercolatorAdapter \\
Expand All @@ -29,6 +30,7 @@ process PERCOLATOR {
-post_processing_tdc \\
-score_type pep \\
-score:fdr $params.run_fdr_cutoff \\
${best_per_spectrum_only} \\
$args \\
2>&1 | tee ${id_file.baseName}_percolator.log

Expand Down
4 changes: 2 additions & 2 deletions modules/local/openms/proteomicslfq/main.nf
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Expand Up @@ -4,8 +4,8 @@ process PROTEOMICSLFQ {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
path(mzmls)
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4 changes: 2 additions & 2 deletions modules/local/openms/sage/main.nf
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Expand Up @@ -4,8 +4,8 @@ process SAGE {
label 'openms'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.06.06' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.06.06' }"
'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2026.07.02' :
'ghcr.io/bigbio/openms-tools-thirdparty:2026.07.02' }"

input:
tuple val(key), val(batch), val(metas), path(mzml_files), path(database)
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4 changes: 2 additions & 2 deletions modules/local/utils/msrescore_features/main.nf
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Expand Up @@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
label 'process_medium'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.20' :
'ghcr.io/bigbio/quantms-rescoring:0.0.20' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.21' :
'ghcr.io/bigbio/quantms-rescoring:0.0.21' }"

input:
tuple val(meta), path(id_files), path(mzml), path(model_weight)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/utils/msrescore_fine_tuning/main.nf
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Expand Up @@ -3,8 +3,8 @@ process MSRESCORE_FINE_TUNING {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.20' :
'ghcr.io/bigbio/quantms-rescoring:0.0.20' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.21' :
'ghcr.io/bigbio/quantms-rescoring:0.0.21' }"

input:
tuple val(meta), path(idparquet), path(mzml), path(ms2_model_dir)
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4 changes: 2 additions & 2 deletions modules/local/utils/psm_clean/main.nf
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Expand Up @@ -3,8 +3,8 @@ process PSM_CLEAN {
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.20' :
'ghcr.io/bigbio/quantms-rescoring:0.0.20' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.21' :
'ghcr.io/bigbio/quantms-rescoring:0.0.21' }"

input:
tuple val(meta), path(idparquet), path(mzml)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/utils/spectrum_features/main.nf
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Expand Up @@ -3,8 +3,8 @@ process SPECTRUM_FEATURES {
label 'process_low'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.20' :
'ghcr.io/bigbio/quantms-rescoring:0.0.20' }"
'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.21' :
'ghcr.io/bigbio/quantms-rescoring:0.0.21' }"

input:
tuple val(meta), path(id_file), path(ms_file)
Expand Down
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