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Merged
d4straub merged 6 commits into from
Jan 22, 2026
+77 −86
Merged

Nextflow strict syntax for non-nf-core-modules/workflows #942

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53fcf5e
adjust DADA2_FILTNTRIM config
d4straub Jan 21, 2026
71b941c
strict syntax for non-nf-core-modules/workflows
d4straub Jan 21, 2026
0552a5e
fix --help
d4straub Jan 21, 2026
81e3f36
nf-core subworkflows update utils_nfschema_plugin
d4straub Jan 22, 2026
16ad89c
revert changes to nf-test.config
d4straub Jan 22, 2026
86098af
update CHANGELOG
d4straub Jan 22, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#942](https://github.com/nf-core/ampliseq/pull/942) - Nextflow strict syntax for non-nf-core-modules/workflows

### `Dependencies`

### `Removed`
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9 changes: 4 additions & 5 deletions conf/modules.config
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Expand Up @@ -137,17 +137,16 @@ process {
]
}

max_len = params.max_len ?: "Inf"
withName: DADA2_FILTNTRIM {
ext.args = [
'maxN = 0, trimRight = 0, minQ = 0, rm.lowcomplex = 0, orient.fwd = NULL, matchIDs = FALSE, id.sep = "\\\\s", id.field = NULL, n = 1e+05, OMP = TRUE',
"qualityType = \"${params.quality_type}\"",
"truncQ = ${params.truncq}",
"minLen = ${params.min_len}",
params.max_len ? "maxLen = ${params.max_len}" : "maxLen = Inf",
params.iontorrent ? "trimLeft = 15" : "trimLeft = 0",
params.pacbio || params.iontorrent || params.single_end ? "maxEE = ${params.max_ee}" : "maxEE = c(${params.max_ee}, ${params.max_ee})",
params.pacbio ? "trimLeft = 0, minLen = ${params.min_len}, maxLen = $max_len, rm.phix = FALSE" :
params.iontorrent ? "trimLeft = 15, minLen = ${params.min_len}, maxLen = $max_len, rm.phix = TRUE" :
params.illumina_pe_its ? "trimLeft = 0, minLen = ${params.min_len}, maxLen = $max_len, rm.phix = TRUE" :
"trimLeft = 0, minLen = ${params.min_len}, maxLen = $max_len, rm.phix = TRUE"
params.pacbio ? "rm.phix = FALSE" : "rm.phix = TRUE"
].join(',').replaceAll('(,)*$', "")
publishDir = [
path: { "${params.outdir}/dada2/args" },
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -124,7 +124,7 @@
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
"git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
"installed_by": ["subworkflows"]
}
}
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2 changes: 0 additions & 2 deletions modules/local/barrnapsummary.nf
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Expand Up @@ -16,8 +16,6 @@ process BARRNAPSUMMARY {


script:
def args = task.ext.args ?: ''

"""
summarize_barrnap.py $predictions

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2 changes: 1 addition & 1 deletion modules/local/qiime2_alphararefaction.nf
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@@ -1,7 +1,7 @@
process QIIME2_ALPHARAREFACTION {
label 'process_low'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_ancom_asv.nf
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Expand Up @@ -5,7 +5,7 @@ process QIIME2_ANCOM_ASV {
label 'process_long'
label 'error_ignore'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_ancom_tax.nf
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Expand Up @@ -3,7 +3,7 @@ process QIIME2_ANCOM_TAX {
label 'process_medium'
label 'process_cpu_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_ancombc_asv.nf
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Expand Up @@ -5,7 +5,7 @@ process QIIME2_ANCOMBC_ASV {
label 'process_long'
label 'error_ignore'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_ancombc_tax.nf
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Expand Up @@ -3,7 +3,7 @@ process QIIME2_ANCOMBC_TAX {
label 'process_medium'
label 'process_cpu_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_barplot.nf
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@@ -1,7 +1,7 @@
process QIIME2_BARPLOT {
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_classify.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_CLASSIFY {
tag "${repseq},${trained_classifier}"
label 'process_huge'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_diversity_adonis.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ADONIS {
tag "${core.baseName}-${formula}"
label 'process_low'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_diversity_alpha.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ALPHA {
tag "${core.baseName}"
label 'process_low'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_diversity_beta.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETA {
tag "${core.baseName}-${category}"
label 'process_low'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_diversity_betaord.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETAORD {
tag "${core.baseName}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_diversity_core.nf
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@@ -1,7 +1,7 @@
process QIIME2_DIVERSITY_CORE {
label 'process_medium'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_export_absolute.nf
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@@ -1,7 +1,7 @@
process QIIME2_EXPORT_ABSOLUTE {
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_export_relasv.nf
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@@ -1,7 +1,7 @@
process QIIME2_EXPORT_RELASV {
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_export_reltax.nf
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@@ -1,7 +1,7 @@
process QIIME2_EXPORT_RELTAX {
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_extract.nf
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Expand Up @@ -3,7 +3,7 @@ process QIIME2_EXTRACT {
label 'process_medium'
label 'process_long'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_featuretable_group.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_FEATURETABLE_GROUP {
tag "${category}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_filtersamples.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_FILTERSAMPLES {
tag "${filter}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_inasv.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_INASV {
tag "${asv}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_inseq.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_INSEQ {
tag "${seq}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_intax.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_INTAX {
tag "${tax}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_intree.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_INTREE {
tag "${meta.id}:${meta.model}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_seqfiltertable.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_SEQFILTERTABLE {
tag "${repseq}-filter-by-${table}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_tablefiltertaxa.nf
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Expand Up @@ -2,7 +2,7 @@ process QIIME2_TABLEFILTERTAXA {
tag "taxa:${exclude_taxa};min-freq:${min_frequency};min-samples:${min_samples}"
label 'process_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_train.nf
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Expand Up @@ -3,7 +3,7 @@ process QIIME2_TRAIN {
label 'process_huge'
label 'process_cpu_single'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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2 changes: 1 addition & 1 deletion modules/local/qiime2_tree.nf
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@@ -1,7 +1,7 @@
process QIIME2_TREE {
label 'process_medium'

conda "${projectDir}/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
conda "${moduleDir}/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml"
container "qiime2/amplicon:2024.10"

input:
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4 changes: 1 addition & 3 deletions modules/local/sidle_align.nf
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Expand Up @@ -2,7 +2,7 @@ process SIDLE_ALIGN {
tag "$meta.region"
label 'process_medium'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
Expand All @@ -15,8 +15,6 @@ process SIDLE_ALIGN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.region}"
def primerfw = "${meta.fw_primer}"
def primerrv = "${meta.rv_primer}"
"""
# https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#regional-alignment
export XDG_CONFIG_HOME="./xdgconfig"
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2 changes: 1 addition & 1 deletion modules/local/sidle_dbextract.nf
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Expand Up @@ -3,7 +3,7 @@ process SIDLE_DBEXTRACT {
tag "$meta.region,$meta.region_length"
label 'process_medium'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
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2 changes: 1 addition & 1 deletion modules/local/sidle_dbfilt.nf
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@@ -1,7 +1,7 @@
process SIDLE_DBFILT {
label 'process_low'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
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4 changes: 2 additions & 2 deletions modules/local/sidle_dbrecon.nf
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@@ -1,7 +1,7 @@
process SIDLE_DBRECON {
label 'process_medium'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
Expand All @@ -19,7 +19,7 @@ process SIDLE_DBRECON {
def args = task.ext.args ?: ''
def db_input = ""
// sort the input so that the regions are sorted by sequence
def df = [metaid, map, aligned_map].transpose().sort{ it[0] }
def df = [metaid, map, aligned_map].transpose().sort()
df.each { i ->
db_input += " --p-region "+i[0]+" --i-kmer-map "+i[1]+" --i-regional-alignment "+i[2]
}
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2 changes: 1 addition & 1 deletion modules/local/sidle_filttax.nf
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Expand Up @@ -2,7 +2,7 @@
process SIDLE_FILTTAX {
label 'process_single'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
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3 changes: 1 addition & 2 deletions modules/local/sidle_in.nf
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Expand Up @@ -2,7 +2,7 @@ process SIDLE_IN {
tag "$meta.region"
label 'process_single'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
Expand All @@ -13,7 +13,6 @@ process SIDLE_IN {
path "versions.yml" , emit: versions

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.region}"
"""
export XDG_CONFIG_HOME="./xdgconfig"
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2 changes: 1 addition & 1 deletion modules/local/sidle_indb.nf
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@@ -1,7 +1,7 @@
process SIDLE_INDB {
label 'process_single'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
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3 changes: 1 addition & 2 deletions modules/local/sidle_indbaligned.nf
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@@ -1,7 +1,7 @@
process SIDLE_INDBALIGNED {
label 'process_single'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
Expand All @@ -12,7 +12,6 @@ process SIDLE_INDBALIGNED {
path "versions.yml" , emit: versions

script:
def args = task.ext.args ?: ''
"""
export XDG_CONFIG_HOME="./xdgconfig"
export MPLCONFIGDIR="./mplconfigdir"
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2 changes: 1 addition & 1 deletion modules/local/sidle_seqrecon.nf
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Expand Up @@ -2,7 +2,7 @@ process SIDLE_SEQRECON {
label 'process_medium'
label 'process_cpu_single'

conda "${projectDir}/modules/local/envs/pipesidle-0-1-0-beta.yml"
conda "${moduleDir}/envs/pipesidle-0-1-0-beta.yml"
container 'nf-core/pipesidle:0.1.0-beta'

input:
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