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AF2 output publishDir separate between base program files and plaintext metrics #453

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AF2 output publishDir separate between base program files and plaintext metrics #453

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895c27b
Sort proteinfold AF2 output into plaintext metrics and full output fr…
keiran-rowell-unsw Jan 29, 2026
a74eef1
default false all the large base program output copying to publishDir…
keiran-rowell-unsw Jan 29, 2026
ff2cc2a
Nextflow uses glob brace expansion, so commands, not a regex |
keiran-rowell-unsw Jan 29, 2026
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38 changes: 30 additions & 8 deletions conf/modules_alphafold2.config
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Original file line number Diff line number Diff line change
Expand Up @@ -55,16 +55,38 @@ process {
].join(' ').trim()
publishDir = [
[
path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}" },
path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
mode: 'copy',
saveAs: { filename ->
if(filename.endsWith('_pae.tsv')){
pattern: '*.pkl',
enabled: params.save_base_output,
],
[
path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
mode: 'copy',
pattern: '*.json',
enabled: params.save_base_output,
],
[
path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
mode: 'copy',
pattern: '*.pdb',
enabled: params.save_base_output,
],
[
path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
mode: 'copy',
pattern: '*.{a3m,sto}',
enabled: params.save_base_output,
],
[
path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/proteinfold_reporting" },
mode: 'copy',
pattern: '*_{plddt,msa,ptm,iptm,pae}.tsv',
saveAs : { filename ->
if(filename.endsWith('_pae.tsv')){
"paes/$filename"
} else if(filename.equals('versions.yml')){
null
} else { filename }
},
pattern: '*.*'
} else { filename }
},
],
[
path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/top_ranked_structures" },
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1 change: 1 addition & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -224,6 +224,7 @@ params {
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
save_base_output = false
email = null
email_on_fail = null
plaintext_email = false
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