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fixed rescoring range bugs #583

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Merged
merged 3 commits into from
Sep 15, 2025
Merged

fixed rescoring range bugs #583

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4d8ffad
Merge pull request #72 from bigbio/dev
daichengxin Aug 14, 2025
f1b1f6c
Merge pull request #73 from bigbio/dev
daichengxin Sep 14, 2025
bc74258
fixed bugs
daichengxin Sep 14, 2025
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3 changes: 1 addition & 2 deletions modules/local/openms/id_ripper/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,11 @@ process ID_RIPPER {
'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"

input:
tuple val(meta), path(id_file), val(qval_score)
tuple val(meta), path(id_file)

output:
val(meta), emit: meta
path("*.idXML"), emit: id_rippers
val("MS:1001491"), emit: qval_score
path "versions.yml", emit: versions
path "*.log", emit: log

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4 changes: 2 additions & 2 deletions subworkflows/local/dda_id/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ workflow DDA_ID {
ch_file_preparation_results.map{[it[0].mzml_id, it[0]]}.set{meta}
ID_RIPPER.out.id_rippers.flatten().map { add_file_prefix (it)}.set{id_rippers}
meta.combine(id_rippers, by: 0)
.map{ [it[1], it[2], "MS:1001491"]}
.map{ [it[1], it[2]]}
.set{ ch_consensus_input }
ch_software_versions = ch_software_versions.mix(ID_RIPPER.out.versions)

Expand Down Expand Up @@ -137,7 +137,7 @@ workflow DDA_ID {
ch_file_preparation_results.map{[it[0].mzml_id, it[0]]}.set{meta}
ID_RIPPER.out.id_rippers.flatten().map { add_file_prefix (it)}.set{id_rippers}
meta.combine(id_rippers, by: 0)
.map{ [it[1], it[2], "MS:1001491"]}
.map{ [it[1], it[2]]}
.set{ ch_consensus_input }
ch_software_versions = ch_software_versions.mix(ID_RIPPER.out.versions)

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4 changes: 2 additions & 2 deletions subworkflows/local/psm_rescoring/main.nf
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Expand Up @@ -80,7 +80,7 @@ workflow PSM_RESCORING {
ch_file_preparation_results.map{[it[0].mzml_id, it[0]]}.set{meta}
ID_RIPPER.out.id_rippers.flatten().map { add_file_prefix (it)}.set{id_rippers}
meta.combine(id_rippers, by: 0)
.map{ [it[1], it[2], "MS:1001491"]}
.map{ [it[1], it[2]]}
.set{ ch_consensus_input }
ch_software_versions = ch_software_versions.mix(ID_RIPPER.out.versions)

Expand Down Expand Up @@ -111,7 +111,7 @@ workflow PSM_RESCORING {
ch_file_preparation_results.map{[it[0].mzml_id, it[0]]}.set{meta}
ID_RIPPER.out.id_rippers.flatten().map { add_file_prefix (it)}.set{id_rippers}
meta.combine(id_rippers, by: 0)
.map{ [it[1], it[2], "MS:1001491"]}
.map{ [it[1], it[2]]}
.set{ ch_consensus_input }
ch_software_versions = ch_software_versions.mix(ID_RIPPER.out.versions)
}
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