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Feature bowtie align genome args #539

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cb0af57
Merge pull request #524 from nf-core/dev
apeltzer Jan 7, 2026
9ec46d0
set bowtie align arguments at launch
piplus2 Apr 28, 2026
e1960c4
update seqcluster module
lpantano Apr 28, 2026
8d4dc57
chore: update snapshots after update seqcluster
piplus2 May 4, 2026
52c6117
fix: force rich==14.2.0 for compatibility with multiqc=1.33
piplus2 May 4, 2026
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5 changes: 5 additions & 0 deletions conf/modules.config
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Expand Up @@ -176,6 +176,11 @@ process {
]
}

// Bowtie align arguments
withName: 'SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME' {
ext.args = params.bowtie_align_args ? params.bowtie_align_args : ''
}

withName: 'CLEAN_FASTA' {
ext.args = "-c fastx '{gsub(/[^ATGCatgc]/, \"N\", \$seq); sub(/ .*/, \"\", \$name); print \">\"\$name\"\\n\"\$seq}'"
ext.prefix = {"${meta.id}_clean.fa"}
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1 change: 1 addition & 0 deletions docs/usage.md
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Expand Up @@ -53,6 +53,7 @@ See examples in: [the test-datasets repository of nf-core](https://github.com/nf

- `fasta`: the reference genome FASTA file
- `bowtie_index`: points to the folder containing the `bowtie` indices for the genome reference specified by `fasta`.
- `bowtie_align_args`: Optional flags to pass to Bowtie 1 for the genome mapping, e.g. `--bowtie_align_args '-v 1 --best'`. Only a subset of Bowtie 1 flags are allowed to keep compatibility with the pipeline. If invalid or disallowed values are included, the pipeline will exit with an error message.

> [!NOTE]
> if the FASTA file in `fasta` is not the same file used to generate the `bowtie` indices, then the pipeline will fail.
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -123,7 +123,7 @@
},
"seqcluster/collapse": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"seqkit/fq2fa": {
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1 change: 1 addition & 0 deletions modules/nf-core/multiqc/environment.yml
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2 changes: 2 additions & 0 deletions modules/nf-core/seqcluster/collapse/environment.yml
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5 changes: 2 additions & 3 deletions modules/nf-core/seqcluster/collapse/main.nf
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4 changes: 4 additions & 0 deletions nextflow.config
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Expand Up @@ -72,6 +72,10 @@ params {
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false

// Bowtie align options
bowtie_align_args = ''

// MultiQC options
multiqc_config = null
multiqc_title = null
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8 changes: 8 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -181,6 +181,14 @@
"fa_icon": "fas fa-book",
"help_text": "Point to the directory created by Bowtie 1 when indexing. Bowtie 1 indices consist of six files:\n\n```bash\ngenome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt\n```\n"
},
"bowtie_align_args": {
"type": "string",
"default": "",
"description": "Additional arguments to pass to Bowtie alignment.",
"help_text": "These flags are passed to Bowtie 1 for the genome mapping, e.g. `--bowtie_align_args '-v 1 --best'`. Use with caution as some flags may conflict with pipeline-managed options.",
"fa_icon": "fas fa-terminal",
"hidden": true
},
"save_reference": {
"type": "boolean",
"description": "Save generated reference genome files to results.",
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97 changes: 97 additions & 0 deletions subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
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Expand Up @@ -105,6 +105,11 @@ workflow PIPELINE_INITIALISATION {
//
validateInputParameters()

//
// Validate the bowtie align arguments provided through params.bowtie_align_args
//
validateBowtieGenomeArgs()

//
// Create channel from input file provided through params.input
//
Expand Down Expand Up @@ -250,6 +255,98 @@ def validateInputSamplesheet(input) {
return [ metas[0], fastqs ]
}
//
// Validate the bowtie align arguments provided through params.bowtie_align_args
//
def validateBowtieGenomeArgs() {
if (!params.bowtie_align_args) return // empty string is fine

// Allowlist: flag -> expected value type (null = flag only, 'int' = requires integer)
def ALLOWED_GENOME_ARGS = [
'-v' : 'int_0_3',
'-n' : 'int_0_3',
'--seedmms' : 'int_0_3',
'-e' : 'int',
'--maqerr' : 'int',
'-l' : 'int',
'--seedlen' : 'int',
'-k' : 'int',
'-m' : 'int',
'--maxbts' : 'int',
'--chunkmbs' : 'int',
'--seed' : 'int',
'--best' : null,
'--strata' : null,
'--nomaqround' : null,
'--norc' : null,
]

// Mutually exclusive pairs
def MUTEX_PAIRS = [
['-v', '-n'],
['-v', '--seedmms'],
['--strata', '--best'], // --strata requires --best, so flag if --strata without --best
]

def tokens = params.bowtie_align_args.trim().split(/\s+/)
def i = 0
def seen = [] as Set

while (i < tokens.size()) {
def token = tokens[i]

// Handle --flag=value syntax by splitting on '='
def flag = token
def value = null
if (token.contains('=')) {
def parts = token.split('=', 2)
flag = parts[0]
value = parts[1]
}

if (!ALLOWED_GENOME_ARGS.containsKey(flag)) {
error "[bowtie_align_args] Argument '${flag}' is not allowed. " +
"Only these flags are permitted: ${ALLOWED_GENOME_ARGS.keySet().sort().join(', ')}"
}

def expectedType = ALLOWED_GENOME_ARGS[flag]
seen << flag

if (expectedType != null) {
// Expect a value — either inline (--flag=val) or next token (--flag val)
if (value == null) {
i++
if (i >= tokens.size()) {
error "[bowtie_align_args] Argument '${flag}' requires a value but none was provided."
}
value = tokens[i]
}

// Validate the value type
if (expectedType == 'int' || expectedType == 'int_0_3') {
if (!(value =~ /^\d+$/)) {
error "[bowtie_align_args] Argument '${flag}' requires an integer value, got '${value}'."
}
if (expectedType == 'int_0_3' && !(value.toInteger() in 0..3)) {
error "[bowtie_align_args] Argument '${flag}' must be between 0 and 3, got '${value}'."
}
}
} else if (value != null) {
// Flag-only arg was given a value via = syntax
error "[bowtie_align_args] Argument '${flag}' does not take a value, got '${value}'."
}

i++
}

// Mutual exclusivity checks
if (seen.contains('-v') && (seen.contains('-n') || seen.contains('--seedmms'))) {
error "[bowtie_align_args] '-v' and '-n'/'--seedmms' are mutually exclusive."
}
if (seen.contains('--strata') && !seen.contains('--best')) {
error "[bowtie_align_args] '--strata' requires '--best' to also be specified."
}
}
//
// Get attribute from genome config file e.g. fasta
//
def getGenomeAttribute(attribute) {
Expand Down
31 changes: 3 additions & 28 deletions tests/default.nf.test.snap
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Expand Up @@ -345,9 +345,6 @@
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/mirtop_mean_read_count_plot.txt",
"multiqc/multiqc_data/mirtop_read_count_plot.txt",
"multiqc/multiqc_data/mirtop_unique_read_count_plot.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc.parquet",
"multiqc/multiqc_data/multiqc_citations.txt",
Expand All @@ -356,7 +353,6 @@
"multiqc/multiqc_data/multiqc_fastqc.txt",
"multiqc/multiqc_data/multiqc_fastqc_fastqc-1.txt",
"multiqc/multiqc_data/multiqc_general_stats.txt",
"multiqc/multiqc_data/multiqc_mirtop.txt",
"multiqc/multiqc_data/multiqc_mirtrace_complexity.txt",
"multiqc/multiqc_data/multiqc_mirtrace_contamination.txt",
"multiqc/multiqc_data/multiqc_mirtrace_length.txt",
Expand Down Expand Up @@ -401,12 +397,6 @@
"multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
"multiqc/multiqc_plots/pdf/mirtop_mean_read_count_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/mirtop_mean_read_count_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/mirtop_read_count_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/mirtop_read_count_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/mirtop_unique_read_count_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/mirtop_unique_read_count_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/samtools-stats-dp.pdf",
"multiqc/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf",
Expand Down Expand Up @@ -444,12 +434,6 @@
"multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
"multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
"multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
"multiqc/multiqc_plots/png/mirtop_mean_read_count_plot-cnt.png",
"multiqc/multiqc_plots/png/mirtop_mean_read_count_plot-pct.png",
"multiqc/multiqc_plots/png/mirtop_read_count_plot-cnt.png",
"multiqc/multiqc_plots/png/mirtop_read_count_plot-pct.png",
"multiqc/multiqc_plots/png/mirtop_unique_read_count_plot-cnt.png",
"multiqc/multiqc_plots/png/mirtop_unique_read_count_plot-pct.png",
"multiqc/multiqc_plots/png/samtools-stats-dp.png",
"multiqc/multiqc_plots/png/samtools_alignment_plot-cnt.png",
"multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png",
Expand Down Expand Up @@ -487,12 +471,6 @@
"multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
"multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
"multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
"multiqc/multiqc_plots/svg/mirtop_mean_read_count_plot-cnt.svg",
"multiqc/multiqc_plots/svg/mirtop_mean_read_count_plot-pct.svg",
"multiqc/multiqc_plots/svg/mirtop_read_count_plot-cnt.svg",
"multiqc/multiqc_plots/svg/mirtop_read_count_plot-pct.svg",
"multiqc/multiqc_plots/svg/mirtop_unique_read_count_plot-cnt.svg",
"multiqc/multiqc_plots/svg/mirtop_unique_read_count_plot-pct.svg",
"multiqc/multiqc_plots/svg/samtools-stats-dp.svg",
"multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg",
"multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg",
Expand Down Expand Up @@ -643,14 +621,11 @@
"fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0",
"fastqc_sequence_length_distribution_plot.txt:md5,f1356c87ed134bdde935faf354b7a9a7",
"fastqc_top_overrepresented_sequences_table.txt:md5,4eb3d5bf770abb0a399bc5710876407b",
"mirtop_mean_read_count_plot.txt:md5,fa4d2c3fe9aac694d2d6d12bf2b844ba",
"mirtop_read_count_plot.txt:md5,835d6b70ae9f61a6e3dcbe369611943f",
"mirtop_unique_read_count_plot.txt:md5,4fc6b7e4f279b0e79a995279d3576682",
"multiqc_citations.txt:md5,ea6d63393b7f47815a949fc58ee0caf8",
"multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57",
"multiqc_fastp.txt:md5,33a1689e5f0f5047da6b28440e121476",
"multiqc_fastqc.txt:md5,74d277d129db4aab9c98790a96a40557",
"multiqc_fastqc_fastqc-1.txt:md5,4c4f6b548ce4f8fdf829a9a086f1ee9f",
"multiqc_general_stats.txt:md5,9f5148b6e5e352814bbc6420efa32573",
"multiqc_general_stats.txt:md5,e20a5b517d415775d152f81cef233f4f",
"multiqc_mirtrace_complexity.txt:md5,2da5d49a2eebc988bf79ba2701982a9d",
"multiqc_mirtrace_contamination.txt:md5,a6f8d6c500f6f53c698d3432297b591d",
"multiqc_mirtrace_length.txt:md5,d740d8d43d3bcfa0bc785f6aa7481da1",
Expand All @@ -670,6 +645,6 @@
"nf-test": "0.9.3",
"nextflow": "25.04.6"
},
"timestamp": "2025-12-16T18:23:20.008558265"
"timestamp": "2026-04-29T22:01:55.005855067"
}
}
33 changes: 4 additions & 29 deletions tests/test_mirgenedb.nf.test.snap
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Expand Up @@ -332,9 +332,6 @@
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/mirtop_mean_read_count_plot.txt",
"multiqc/multiqc_data/mirtop_read_count_plot.txt",
"multiqc/multiqc_data/mirtop_unique_read_count_plot.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc.parquet",
"multiqc/multiqc_data/multiqc_citations.txt",
Expand All @@ -343,7 +340,6 @@
"multiqc/multiqc_data/multiqc_fastqc.txt",
"multiqc/multiqc_data/multiqc_fastqc_fastqc-1.txt",
"multiqc/multiqc_data/multiqc_general_stats.txt",
"multiqc/multiqc_data/multiqc_mirtop.txt",
"multiqc/multiqc_data/multiqc_samtools_stats.txt",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
Expand Down Expand Up @@ -384,12 +380,6 @@
"multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
"multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
"multiqc/multiqc_plots/pdf/mirtop_mean_read_count_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/mirtop_mean_read_count_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/mirtop_read_count_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/mirtop_read_count_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/mirtop_unique_read_count_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/mirtop_unique_read_count_plot-pct.pdf",
"multiqc/multiqc_plots/pdf/samtools-stats-dp.pdf",
"multiqc/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf",
"multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf",
Expand Down Expand Up @@ -427,12 +417,6 @@
"multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
"multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
"multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
"multiqc/multiqc_plots/png/mirtop_mean_read_count_plot-cnt.png",
"multiqc/multiqc_plots/png/mirtop_mean_read_count_plot-pct.png",
"multiqc/multiqc_plots/png/mirtop_read_count_plot-cnt.png",
"multiqc/multiqc_plots/png/mirtop_read_count_plot-pct.png",
"multiqc/multiqc_plots/png/mirtop_unique_read_count_plot-cnt.png",
"multiqc/multiqc_plots/png/mirtop_unique_read_count_plot-pct.png",
"multiqc/multiqc_plots/png/samtools-stats-dp.png",
"multiqc/multiqc_plots/png/samtools_alignment_plot-cnt.png",
"multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png",
Expand Down Expand Up @@ -470,12 +454,6 @@
"multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
"multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
"multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
"multiqc/multiqc_plots/svg/mirtop_mean_read_count_plot-cnt.svg",
"multiqc/multiqc_plots/svg/mirtop_mean_read_count_plot-pct.svg",
"multiqc/multiqc_plots/svg/mirtop_read_count_plot-cnt.svg",
"multiqc/multiqc_plots/svg/mirtop_read_count_plot-pct.svg",
"multiqc/multiqc_plots/svg/mirtop_unique_read_count_plot-cnt.svg",
"multiqc/multiqc_plots/svg/mirtop_unique_read_count_plot-pct.svg",
"multiqc/multiqc_plots/svg/samtools-stats-dp.svg",
"multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg",
"multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg",
Expand Down Expand Up @@ -569,14 +547,11 @@
"fastqc_sequence_duplication_levels_plot.txt:md5,2b1cbdce195d2aedc4bff4c5e9b618d4",
"fastqc_sequence_length_distribution_plot.txt:md5,6bd21067e3ab28cd33ac107417e72c4c",
"fastqc_top_overrepresented_sequences_table.txt:md5,91b745155fb6c1652cdd8222fc96a9cc",
"mirtop_mean_read_count_plot.txt:md5,13fc23549fa91434e7cc87ea413022eb",
"mirtop_read_count_plot.txt:md5,2aa7167a13f4db1799736bc7150b7efd",
"mirtop_unique_read_count_plot.txt:md5,3bc374b16585d00654cde12fb7f5a363",
"multiqc_citations.txt:md5,ea6d63393b7f47815a949fc58ee0caf8",
"multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57",
"multiqc_fastp.txt:md5,19649c8fcacf031058beb4574e7757f6",
"multiqc_fastqc.txt:md5,5f3d48b29b7909fd7f0c4da6f8745c08",
"multiqc_fastqc_fastqc-1.txt:md5,ca8352d25077b529780f4dfa79f343a6",
"multiqc_general_stats.txt:md5,0088299b96f9b7e15d23a91228d676d2",
"multiqc_general_stats.txt:md5,b4d1b4edcf34fcbadce157bf5b4fb7f0",
"multiqc_samtools_stats.txt:md5,805d665c8ecc0a099111166581f43c07",
"samtools-stats-dp.txt:md5,f263d0f3e065cbc1a7089887ac24938f",
"samtools_alignment_plot.txt:md5,f516084a276f0931165b93724d3735ad"
Expand Down Expand Up @@ -608,8 +583,8 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.6"
"nextflow": "25.04.2"
},
"timestamp": "2025-12-16T17:00:25.99408485"
"timestamp": "2026-04-30T09:13:45.941037731"
}
}
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