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Merged
LilyAnderssonLee merged 4 commits into from
Oct 3, 2025
Merged

Enable runs for PACBIO_SMRT #653

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c6fe9bc
Enable runs for PACBIO-SMRT data
LilyAnderssonLee Sep 26, 2025
9172886
update the changelog
LilyAnderssonLee Sep 29, 2025
f1448f5
update docs
LilyAnderssonLee Oct 2, 2025
267c893
run FASTQC/FALCO for pacbio data
LilyAnderssonLee Oct 3, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#653](https://github.com/nf-core/taxprofiler/pull/653) Enable runs for `PACBIO_SMRT`data (fixed by @LilyAnderssonLee)

### `Changed`

### `Dependencies`
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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -30,7 +30,7 @@ Please see the rest of this page for information about how to prepare input samp

## Samplesheet inputs

nf-core/taxprofiler can accept as input raw or preprocessed single- or paired-end short-read (e.g. Illumina) FASTQ files, long-read FASTQ files (e.g. Oxford Nanopore), or FASTA sequences (available for a subset of profilers).
nf-core/taxprofiler can accept as input raw or preprocessed single- or paired-end short-read (e.g. Illumina) FASTQ files, long-read FASTQ files (e.g. Oxford Nanopore), or FASTA sequences (available for a subset of profilers). For PACBIO_SMRT data, please convert BAM files to FASTQ format before input.

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below. Furthermore, nf-core/taxprofiler also requires a second comma-separated file of 3 columns with a header row as in the examples below.

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26 changes: 13 additions & 13 deletions subworkflows/local/profiling.nf
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Expand Up @@ -152,10 +152,10 @@ workflow PROFILING {
[meta, input_reads, db_meta_new, db]
}
.filter { meta, _input_reads, db_meta_new, _db ->
if (db_meta_new.tool == 'bracken' && meta.instrument_platform == 'OXFORD_NANOPORE') {
log.warn("[nf-core/taxprofiler] Bracken has not been evaluated for Nanopore data. Skipping Bracken for sample ${meta.id}.")
if (db_meta_new.tool == 'bracken' && (meta.instrument_platform == 'OXFORD_NANOPORE' || meta.instrument_platform == 'PACBIO_SMRT')) {
log.warn("[nf-core/taxprofiler] Bracken has not been evaluated for long-read datasets. Skipping Bracken for sample ${meta.id}.")
}
db_meta_new.tool == 'kraken2' || (db_meta_new.tool == 'bracken' && meta.instrument_platform != 'OXFORD_NANOPORE')
db_meta_new.tool == 'kraken2' || (db_meta_new.tool == 'bracken' && (meta.instrument_platform != 'OXFORD_NANOPORE' && meta.instrument_platform != 'PACBIO_SMRT'))
}

ch_input_for_kraken2 = ch_prepare_for_kraken2.multiMap { it ->
Expand Down Expand Up @@ -378,25 +378,25 @@ workflow PROFILING {

ch_input_for_kmcp = ch_input_for_profiling.kmcp
.filter { meta, _input_reads, meta_db, _db ->
if (meta['instrument_platform'] == 'OXFORD_NANOPORE') {
if (meta.instrument_platform == 'OXFORD_NANOPORE' || meta.instrument_platform == 'PACBIO_SMRT') {
log.warn("[nf-core/taxprofiler] KMCP is only suitable for short-read metagenomic profiling, with much lower sensitivity on long-read datasets. Skipping KMCP for sample ${meta.id}.")
}
meta_db['tool'] == 'kmcp' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
meta_db.tool == 'kmcp' && (meta.instrument_platform != 'OXFORD_NANOPORE' && meta.instrument_platform != 'PACBIO_SMRT')
}
.map { meta, input_reads, db_meta, db ->
def db_meta_keys = db_meta.keySet()
def db_meta_new = db_meta.subMap(db_meta_keys)

// Split the string, the arguments before semicolon should be parsed into kmcp search
def parsed_params = db_meta_new['db_params'].split(";")
def parsed_params = db_meta_new.db_params.split(";")
if (parsed_params.size() == 2) {
db_meta_new['db_params'] = parsed_params[0]
db_meta_new.db_params = parsed_params[0]
}
else if (parsed_params.size() == 0) {
db_meta_new['db_params'] = ""
db_meta_new.db_params = ""
}
else {
db_meta_new['db_params'] = parsed_params[0]
db_meta_new.db_params = parsed_params[0]
}

[meta, input_reads, db_meta_new, db]
Expand Down Expand Up @@ -424,7 +424,7 @@ workflow PROFILING {
def db_meta_keys = db_meta.keySet()
def db_meta_new = db_meta.subMap(db_meta_keys)

def parsed_params = db_meta['db_params'].split(";")
def parsed_params = db_meta.db_params.split(";")

if (parsed_params.size() == 2) {
db_meta_new = db_meta + [db_params: parsed_params[1]]
Expand Down Expand Up @@ -452,10 +452,10 @@ workflow PROFILING {

ch_input_for_ganonclassify = ch_input_for_profiling.ganon
.filter { meta, _input_reads, meta_db, _db ->
if (meta.instrument_platform == 'OXFORD_NANOPORE') {
log.warn("[nf-core/taxprofiler] Ganon has not been evaluated for Nanopore data. Skipping Ganon for sample ${meta.id}.")
if (meta.instrument_platform == 'OXFORD_NANOPORE' || meta.instrument_platform == 'PACBIO_SMRT') {
log.warn("[nf-core/taxprofiler] Ganon has not been evaluated for long-read datasets. Skipping Ganon for sample ${meta.id}.")
}
meta_db.tool == 'ganon' && meta.instrument_platform != 'OXFORD_NANOPORE'
meta_db.tool == 'ganon' && (meta.instrument_platform != 'OXFORD_NANOPORE' && meta.instrument_platform != 'PACBIO_SMRT')
}
.multiMap { it ->
reads: [it[0] + it[2], it[1]]
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18 changes: 12 additions & 6 deletions workflows/taxprofiler.nf
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Expand Up @@ -84,7 +84,7 @@ workflow TAXPROFILER {
meta.instrument_platform = instrument_platform

// Define single_end based on the conditions
meta.single_end = (fastq_1 && !fastq_2 && instrument_platform != 'OXFORD_NANOPORE')
meta.single_end = (fastq_1 && !fastq_2 && instrument_platform != 'OXFORD_NANOPORE' && instrument_platform != 'PACBIO_SMRT')

// Define is_fasta based on the presence of fasta
meta.is_fasta = fasta ? true : false
Expand All @@ -95,6 +95,9 @@ workflow TAXPROFILER {
if (meta.instrument_platform == 'OXFORD_NANOPORE' && fastq_2) {
error("Error: Please check input samplesheet: for Oxford Nanopore reads entry `fastq_2` should be empty!")
}
if (meta.instrument_platform == 'PACBIO_SMRT' && fastq_2) {
error("Error: Please check input samplesheet: for PacBio reads entry `fastq_2` should be empty!")
}
if (meta.single_end && fastq_2) {
error("Error: Please check input samplesheet: for single-end reads entry `fastq_2` should be empty")
}
Expand All @@ -106,16 +109,19 @@ workflow TAXPROFILER {
nanopore: instrument_platform == 'OXFORD_NANOPORE' && !meta.is_fasta
meta.single_end = true
return [meta + [type: "long"], [fastq_1]]
pacbio: instrument_platform == 'PACBIO_SMRT' && !meta.is_fasta
meta.single_end = true
return [meta + [type: "long"], [fastq_1]]
fasta_short: meta.is_fasta && instrument_platform == 'ILLUMINA'
meta.single_end = true
return [meta + [type: "short"], [fasta]]
fasta_long: meta.is_fasta && instrument_platform == 'OXFORD_NANOPORE'
fasta_long: meta.is_fasta && (instrument_platform == 'OXFORD_NANOPORE' || instrument_platform == 'PACBIO_SMRT')
meta.single_end = true
return [meta + [type: "long"], [fasta]]
}

// Merge ch_input.fastq and ch_input.nanopore into a single channel
ch_input_for_fastqc = ch_input.fastq.mix(ch_input.nanopore)
ch_input_for_fastqc = ch_input.fastq.mix(ch_input.nanopore, ch_input.pacbio )

// Validate and decompress databases
ch_dbs_for_untar = databases.branch { db_meta, db_path ->
Expand Down Expand Up @@ -184,11 +190,11 @@ workflow TAXPROFILER {
}

if (params.perform_longread_qc) {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING(ch_input.nanopore).reads.map { it -> [it[0], [it[1]]] }
ch_longreads_preprocessed_nanopore = LONGREAD_PREPROCESSING(ch_input.nanopore).reads.map { it -> [it[0], [it[1]]] }
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions)
}
else {
ch_longreads_preprocessed = ch_input.nanopore
ch_longreads_preprocessed_nanopore = ch_input.nanopore
}

/*
Expand Down Expand Up @@ -224,7 +230,7 @@ workflow TAXPROFILER {
else {
ch_shortreads_hostremoved = ch_shortreads_filtered
}

ch_longreads_preprocessed = ch_longreads_preprocessed_nanopore.mix(ch_input.pacbio)
if (params.perform_longread_hostremoval) {
ch_longreads_hostremoved = LONGREAD_HOSTREMOVAL(ch_longreads_preprocessed, ch_reference, ch_longread_reference_index).reads
ch_versions = ch_versions.mix(LONGREAD_HOSTREMOVAL.out.versions)
Expand Down