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Merged
jfy133 merged 6 commits into from
Jan 21, 2026
Merged

Make pipeline nextflow strict syntax compliant #510

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e430f4d
Replace `Channel` with `channel`
jfy133 Jan 14, 2026
57b1acf
Merge branch 'dev' into nextflow-strict-syntax
jfy133 Jan 14, 2026
809dbbc
Use proper variable name
jfy133 Jan 14, 2026
5196023
Update RGI to be syntax compliant
jfy133 Jan 14, 2026
f84cab0
Fix comments fro @maxulysse
jfy133 Jan 21, 2026
548a41c
Missing files
jfy133 Jan 21, 2026
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9 changes: 7 additions & 2 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,11 @@
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"installed_by": ["modules"]
},
"gecco/convert": {
"branch": "master",
"git_sha": "2aa243bd8a9b20122ed6fb5d2d3c75b963eef171",
"installed_by": ["modules"]
},
"gecco/run": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
Expand Down Expand Up @@ -192,12 +197,12 @@
},
"rgi/cardannotation": {
"branch": "master",
"git_sha": "531d8a465158c5842f416623017997462a240e16",
"git_sha": "70c072e30155e7671be828762be16576bd4afca7",
"installed_by": ["modules"]
},
"rgi/main": {
"branch": "master",
"git_sha": "531d8a465158c5842f416623017997462a240e16",
"git_sha": "70c072e30155e7671be828762be16576bd4afca7",
"installed_by": ["modules"]
},
"seqkit/seq": {
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/rgi/cardannotation/main.nf
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4 changes: 2 additions & 2 deletions modules/nf-core/rgi/main/main.nf
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214 changes: 109 additions & 105 deletions subworkflows/local/amp.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,164 +2,168 @@
Run AMP screening tools
*/

include { MACREL_CONTIGS } from '../../modules/nf-core/macrel/contigs/main'
include { HMMER_HMMSEARCH as AMP_HMMER_HMMSEARCH } from '../../modules/nf-core/hmmer/hmmsearch/main'
include { AMPLIFY_PREDICT } from '../../modules/nf-core/amplify/predict/main'
include { AMPIR } from '../../modules/nf-core/ampir/main'
include { AMP_DATABASE_DOWNLOAD } from '../../modules/local/amp_database_download'
include { AMPCOMBI2_PARSETABLES } from '../../modules/nf-core/ampcombi2/parsetables'
include { AMPCOMBI2_COMPLETE } from '../../modules/nf-core/ampcombi2/complete'
include { AMPCOMBI2_CLUSTER } from '../../modules/nf-core/ampcombi2/cluster'
include { GUNZIP as GUNZIP_MACREL_PRED ; GUNZIP as GUNZIP_MACREL_ORFS } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as AMP_GUNZIP_HMMER_HMMSEARCH } from '../../modules/nf-core/gunzip/main'
include { TABIX_BGZIP as AMP_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip/main'
include { MERGE_TAXONOMY_AMPCOMBI } from '../../modules/local/merge_taxonomy_ampcombi'
include { MACREL_CONTIGS } from '../../modules/nf-core/macrel/contigs'
include { HMMER_HMMSEARCH as AMP_HMMER_HMMSEARCH } from '../../modules/nf-core/hmmer/hmmsearch'
include { AMPLIFY_PREDICT } from '../../modules/nf-core/amplify/predict'
include { AMPIR } from '../../modules/nf-core/ampir'
include { AMP_DATABASE_DOWNLOAD } from '../../modules/local/amp_database_download'
include { AMPCOMBI2_PARSETABLES } from '../../modules/nf-core/ampcombi2/parsetables'
include { AMPCOMBI2_COMPLETE } from '../../modules/nf-core/ampcombi2/complete'
include { AMPCOMBI2_CLUSTER } from '../../modules/nf-core/ampcombi2/cluster'
include { GUNZIP as GUNZIP_MACREL_PRED ; GUNZIP as GUNZIP_MACREL_ORFS } from '../../modules/nf-core/gunzip'
include { GUNZIP as AMP_GUNZIP_HMMER_HMMSEARCH } from '../../modules/nf-core/gunzip'
include { TABIX_BGZIP as AMP_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip'
include { MERGE_TAXONOMY_AMPCOMBI } from '../../modules/local/merge_taxonomy_ampcombi'

workflow AMP {
take:
fastas // tuple val(meta), path(contigs)
faas // tuple val(meta), path(PROKKA/PRODIGAL.out.faa)
tsvs // tuple val(meta), path(MMSEQS_CREATETSV.out.tsv)
gbks // tuple val(meta), path(ANNOTATION_ANNOTATION_TOOL.out.gbk)
tsvs_interpro // tuple val(meta), path(INTERPROSCAN.out.tsv)'
fastas // tuple val(meta), path(contigs)
faas // tuple val(meta), path(PROKKA/PRODIGAL.out.faa)
tsvs // tuple val(meta), path(MMSEQS_CREATETSV.out.tsv)
gbks // tuple val(meta), path(ANNOTATION_ANNOTATION_TOOL.out.gbk)
tsvs_interpro // tuple val(meta), path(INTERPROSCAN.out.tsv)'

main:
ch_versions = Channel.empty()
ch_ampresults_for_ampcombi = Channel.empty()
ch_macrel_faa = Channel.empty()
ch_ampcombi_summaries = Channel.empty()
ch_ampcombi_complete = null
ch_versions = channel.empty()
ch_ampresults_for_ampcombi = channel.empty()
ch_macrel_faa = channel.empty()
ch_ampcombi_summaries = channel.empty()
ch_ampcombi_complete = null

// When adding new tool that requires FAA, make sure to update conditions
// in funcscan.nf around annotation and AMP subworkflow execution
// to ensure annotation is executed!
ch_faa_for_amplify = faas
ch_faa_for_amp_hmmsearch = faas
ch_faa_for_ampir = faas
ch_faa_for_ampcombi = faas
ch_gbk_for_ampcombi = gbks
ch_interpro_for_ampcombi = tsvs_interpro
ch_faa_for_amplify = faas
ch_faa_for_amp_hmmsearch = faas
ch_faa_for_ampir = faas
ch_faa_for_ampcombi = faas
ch_gbk_for_ampcombi = gbks
ch_interpro_for_ampcombi = tsvs_interpro

// AMPLIFY
if ( !params.amp_skip_amplify ) {
AMPLIFY_PREDICT ( ch_faa_for_amplify, [] )
ch_versions = ch_versions.mix( AMPLIFY_PREDICT.out.versions )
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix( AMPLIFY_PREDICT.out.tsv )
if (!params.amp_skip_amplify) {
AMPLIFY_PREDICT(ch_faa_for_amplify, [])
ch_versions = ch_versions.mix(AMPLIFY_PREDICT.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(AMPLIFY_PREDICT.out.tsv)
}

// MACREL
if ( !params.amp_skip_macrel ) {
MACREL_CONTIGS ( fastas )
ch_versions = ch_versions.mix( MACREL_CONTIGS.out.versions )
GUNZIP_MACREL_PRED ( MACREL_CONTIGS.out.amp_prediction )
GUNZIP_MACREL_ORFS ( MACREL_CONTIGS.out.all_orfs )
ch_versions = ch_versions.mix( GUNZIP_MACREL_PRED.out.versions )
ch_versions = ch_versions.mix( GUNZIP_MACREL_ORFS.out.versions )
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix( GUNZIP_MACREL_PRED.out.gunzip )
ch_macrel_faa = ch_macrel_faa.mix( GUNZIP_MACREL_ORFS.out.gunzip )
ch_faa_for_ampcombi = ch_faa_for_ampcombi.mix( ch_macrel_faa )
if (!params.amp_skip_macrel) {
MACREL_CONTIGS(fastas)
ch_versions = ch_versions.mix(MACREL_CONTIGS.out.versions)
GUNZIP_MACREL_PRED(MACREL_CONTIGS.out.amp_prediction)
GUNZIP_MACREL_ORFS(MACREL_CONTIGS.out.all_orfs)
ch_versions = ch_versions.mix(GUNZIP_MACREL_PRED.out.versions)
ch_versions = ch_versions.mix(GUNZIP_MACREL_ORFS.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(GUNZIP_MACREL_PRED.out.gunzip)
ch_macrel_faa = ch_macrel_faa.mix(GUNZIP_MACREL_ORFS.out.gunzip)
ch_faa_for_ampcombi = ch_faa_for_ampcombi.mix(ch_macrel_faa)
}

// AMPIR
if ( !params.amp_skip_ampir ) {
AMPIR ( ch_faa_for_ampir, params.amp_ampir_model, params.amp_ampir_minlength, 0.0 )
ch_versions = ch_versions.mix( AMPIR.out.versions )
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix( AMPIR.out.amps_tsv )
if (!params.amp_skip_ampir) {
AMPIR(ch_faa_for_ampir, params.amp_ampir_model, params.amp_ampir_minlength, 0.0)
ch_versions = ch_versions.mix(AMPIR.out.versions)
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(AMPIR.out.amps_tsv)
}

// HMMSEARCH
if ( params.amp_run_hmmsearch ) {
if ( params.amp_hmmsearch_models ) { ch_amp_hmm_models = Channel.fromPath( params.amp_hmmsearch_models, checkIfExists: true ) } else { error('[nf-core/funcscan] error: HMM model files not found for --amp_hmmsearch_models! Please check input.') }

ch_amp_hmm_models_meta = ch_amp_hmm_models
.map {
file ->
def meta = [:]
meta['id'] = file.extension == 'gz' ? file.name - '.hmm.gz' : file.name - '.hmm'
[ meta, file ]
}
if (params.amp_run_hmmsearch) {
if (params.amp_hmmsearch_models) {
ch_amp_hmm_models = channel.fromPath(params.amp_hmmsearch_models, checkIfExists: true)
}
else {
error('[nf-core/funcscan] error: HMM model files not found for --amp_hmmsearch_models! Please check input.')
}

ch_amp_hmm_models_meta = ch_amp_hmm_models.map { file ->
def meta = [:]
meta['id'] = file.extension == 'gz' ? file.name - '.hmm.gz' : file.name - '.hmm'
[meta, file]
}

ch_in_for_amp_hmmsearch = ch_faa_for_amp_hmmsearch
.combine( ch_amp_hmm_models_meta )
.map {
meta_faa, faa, meta_hmm, hmm ->
def meta_new = [:]
meta_new['id'] = meta_faa['id']
meta_new['hmm_id'] = meta_hmm['id']
[ meta_new, hmm, faa, params.amp_hmmsearch_savealignments, params.amp_hmmsearch_savetargets, params.amp_hmmsearch_savedomains ]
}

AMP_HMMER_HMMSEARCH ( ch_in_for_amp_hmmsearch )
ch_versions = ch_versions.mix( AMP_HMMER_HMMSEARCH.out.versions )
AMP_GUNZIP_HMMER_HMMSEARCH ( AMP_HMMER_HMMSEARCH.out.output )
ch_versions = ch_versions.mix( AMP_GUNZIP_HMMER_HMMSEARCH.out.versions )
ch_AMP_GUNZIP_HMMER_HMMSEARCH = AMP_GUNZIP_HMMER_HMMSEARCH.out.gunzip
.map { meta, file ->
[ [id: meta.id], file ]
.combine(ch_amp_hmm_models_meta)
.map { meta_faa, faa, meta_hmm, hmm ->
def meta_new = [:]
meta_new['id'] = meta_faa['id']
meta_new['hmm_id'] = meta_hmm['id']
[meta_new, hmm, faa, params.amp_hmmsearch_savealignments, params.amp_hmmsearch_savetargets, params.amp_hmmsearch_savedomains]
}
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix( ch_AMP_GUNZIP_HMMER_HMMSEARCH )

AMP_HMMER_HMMSEARCH(ch_in_for_amp_hmmsearch)
ch_versions = ch_versions.mix(AMP_HMMER_HMMSEARCH.out.versions)
AMP_GUNZIP_HMMER_HMMSEARCH(AMP_HMMER_HMMSEARCH.out.output)
ch_versions = ch_versions.mix(AMP_GUNZIP_HMMER_HMMSEARCH.out.versions)
ch_AMP_GUNZIP_HMMER_HMMSEARCH = AMP_GUNZIP_HMMER_HMMSEARCH.out.gunzip.map { meta, file ->
[[id: meta.id], file]
}
ch_ampresults_for_ampcombi = ch_ampresults_for_ampcombi.mix(ch_AMP_GUNZIP_HMMER_HMMSEARCH)
}

// AMPCOMBI2
ch_input_for_ampcombi = ch_ampresults_for_ampcombi
.groupTuple()
.join( ch_faa_for_ampcombi )
.join( ch_gbk_for_ampcombi )
.join( ch_interpro_for_ampcombi )
.multiMap{
input: [ it[0], it[1] ]
.join(ch_faa_for_ampcombi)
.join(ch_gbk_for_ampcombi)
.join(ch_interpro_for_ampcombi)
.multiMap {
input: [it[0], it[1]]
faa: it[2]
gbk: it[3]
interpro: it [4]
interpro: it[4]
}

// AMPCOMBI2::PARSETABLES
if ( params.amp_ampcombi_db != null ) {
AMPCOMBI2_PARSETABLES ( ch_input_for_ampcombi.input, ch_input_for_ampcombi.faa, ch_input_for_ampcombi.gbk, params.amp_ampcombi_db_id, params.amp_ampcombi_db, ch_input_for_ampcombi.interpro )
} else {
AMP_DATABASE_DOWNLOAD( params.amp_ampcombi_db_id )
ch_versions = ch_versions.mix( AMP_DATABASE_DOWNLOAD.out.versions )
if (params.amp_ampcombi_db != null) {
AMPCOMBI2_PARSETABLES(ch_input_for_ampcombi.input, ch_input_for_ampcombi.faa, ch_input_for_ampcombi.gbk, params.amp_ampcombi_db_id, params.amp_ampcombi_db, ch_input_for_ampcombi.interpro)
}
else {
AMP_DATABASE_DOWNLOAD(params.amp_ampcombi_db_id)
ch_versions = ch_versions.mix(AMP_DATABASE_DOWNLOAD.out.versions)
ch_ampcombi_input_db = AMP_DATABASE_DOWNLOAD.out.db
AMPCOMBI2_PARSETABLES ( ch_input_for_ampcombi.input, ch_input_for_ampcombi.faa, ch_input_for_ampcombi.gbk, params.amp_ampcombi_db_id, ch_ampcombi_input_db, ch_input_for_ampcombi.interpro )
AMPCOMBI2_PARSETABLES(ch_input_for_ampcombi.input, ch_input_for_ampcombi.faa, ch_input_for_ampcombi.gbk, params.amp_ampcombi_db_id, ch_ampcombi_input_db, ch_input_for_ampcombi.interpro)
}
ch_versions = ch_versions.mix( AMPCOMBI2_PARSETABLES.out.versions )
ch_versions = ch_versions.mix(AMPCOMBI2_PARSETABLES.out.versions)

ch_ampcombi_summaries = AMPCOMBI2_PARSETABLES.out.tsv.map{ it[1] }.collect()
ch_ampcombi_summaries = AMPCOMBI2_PARSETABLES.out.tsv.map { it[1] }.collect()

// AMPCOMBI2::COMPLETE
ch_summary_count = ch_ampcombi_summaries.map { it.size() }.sum()

if ( ch_summary_count == 0 || ch_summary_count == 1 ) {
if (ch_summary_count == 0 || ch_summary_count == 1) {
log.warn("[nf-core/funcscan] AMPCOMBI2: ${ch_summary_count} file(s) passed. Skipping AMPCOMBI2_COMPLETE, AMPCOMBI2_CLUSTER, and TAXONOMY MERGING steps.")
} else {
}
else {
AMPCOMBI2_COMPLETE(ch_ampcombi_summaries)
ch_versions = ch_versions.mix( AMPCOMBI2_COMPLETE.out.versions )
ch_ampcombi_complete = AMPCOMBI2_COMPLETE.out.tsv
.filter { file -> file.countLines() > 1 }
ch_versions = ch_versions.mix(AMPCOMBI2_COMPLETE.out.versions)
ch_ampcombi_complete = AMPCOMBI2_COMPLETE.out.tsv.filter { file -> file.countLines() > 1 }
}

// AMPCOMBI2::CLUSTER
if ( ch_ampcombi_complete != null ) {
AMPCOMBI2_CLUSTER ( ch_ampcombi_complete )
ch_versions = ch_versions.mix( AMPCOMBI2_CLUSTER.out.versions )
} else {
if (ch_ampcombi_complete != null) {
AMPCOMBI2_CLUSTER(ch_ampcombi_complete)
ch_versions = ch_versions.mix(AMPCOMBI2_CLUSTER.out.versions)
}
else {
log.warn("[nf-core/funcscan] No AMP hits were found in the samples and so no clustering will be applied.")
}

// MERGE_TAXONOMY
if ( params.run_taxa_classification && ch_ampcombi_complete == null ) {
if (params.run_taxa_classification && ch_ampcombi_complete == null) {
log.warn("[nf-core/funcscan] No AMP hits were found in the samples, therefore no Taxonomy will be merged ")
} else if ( params.run_taxa_classification && ch_ampcombi_complete != null ) {
ch_mmseqs_taxonomy_list = tsvs.map{ it[1] }.collect()
}
else if (params.run_taxa_classification && ch_ampcombi_complete != null) {
ch_mmseqs_taxonomy_list = tsvs.map { it[1] }.collect()

MERGE_TAXONOMY_AMPCOMBI( AMPCOMBI2_CLUSTER.out.cluster_tsv, ch_mmseqs_taxonomy_list )
ch_versions = ch_versions.mix( MERGE_TAXONOMY_AMPCOMBI.out.versions )
MERGE_TAXONOMY_AMPCOMBI(AMPCOMBI2_CLUSTER.out.cluster_tsv, ch_mmseqs_taxonomy_list)
ch_versions = ch_versions.mix(MERGE_TAXONOMY_AMPCOMBI.out.versions)

ch_tabix_input = Channel.of( [ 'id':'ampcombi_complete_summary_taxonomy' ] )
.combine( MERGE_TAXONOMY_AMPCOMBI.out.tsv )
ch_tabix_input = channel.of(['id': 'ampcombi_complete_summary_taxonomy'])
.combine(MERGE_TAXONOMY_AMPCOMBI.out.tsv)

AMP_TABIX_BGZIP( ch_tabix_input )
ch_versions = ch_versions.mix( AMP_TABIX_BGZIP.out.versions )
AMP_TABIX_BGZIP(ch_tabix_input)
ch_versions = ch_versions.mix(AMP_TABIX_BGZIP.out.versions)
}

emit:
Expand Down
28 changes: 14 additions & 14 deletions subworkflows/local/annotation.nf
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Expand Up @@ -2,25 +2,25 @@
Run annotation tools
*/

include { PROKKA } from '../../modules/nf-core/prokka/main'
include { PRODIGAL } from '../../modules/nf-core/prodigal/main'
include { PYRODIGAL } from '../../modules/nf-core/pyrodigal/main'
include { BAKTA_BAKTADBDOWNLOAD } from '../../modules/nf-core/bakta/baktadbdownload/main'
include { BAKTA_BAKTA } from '../../modules/nf-core/bakta/bakta/main'
include { GUNZIP as GUNZIP_PRODIGAL_FNA } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_PRODIGAL_FAA } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_PRODIGAL_GBK } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_PYRODIGAL_FNA } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_PYRODIGAL_FAA } from '../../modules/nf-core/gunzip/main'
include { GUNZIP as GUNZIP_PYRODIGAL_GBK } from '../../modules/nf-core/gunzip/main'
include { PROKKA } from '../../modules/nf-core/prokka'
include { PRODIGAL } from '../../modules/nf-core/prodigal'
include { PYRODIGAL } from '../../modules/nf-core/pyrodigal'
include { BAKTA_BAKTADBDOWNLOAD } from '../../modules/nf-core/bakta/baktadbdownload'
include { BAKTA_BAKTA } from '../../modules/nf-core/bakta/bakta'
include { GUNZIP as GUNZIP_PRODIGAL_FNA } from '../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_PRODIGAL_FAA } from '../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_PRODIGAL_GBK } from '../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_PYRODIGAL_FNA } from '../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_PYRODIGAL_FAA } from '../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_PYRODIGAL_GBK } from '../../modules/nf-core/gunzip'

workflow ANNOTATION {
take:
fasta // tuple val(meta), path(contigs)

main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_versions = channel.empty()
ch_multiqc_files = channel.empty()

if (params.annotation_tool == "pyrodigal" || (params.annotation_tool == "prodigal" && params.run_bgc_screening == true && (!params.bgc_skip_antismash || !params.bgc_skip_deepbgc || !params.bgc_skip_gecco)) || (params.annotation_tool == "prodigal" && params.run_amp_screening == true)) {
// Need to use Pyrodigal for most BGC tools and AMPcombi because Prodigal GBK annotation format is incompatible with them.
Expand Down Expand Up @@ -71,7 +71,7 @@ workflow ANNOTATION {

// BAKTA prepare download
if (params.annotation_bakta_db) {
ch_bakta_db = Channel.fromPath(params.annotation_bakta_db, checkIfExists: true)
ch_bakta_db = channel.fromPath(params.annotation_bakta_db, checkIfExists: true)
.first()
}
else {
Expand Down
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