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remove support for legacy sample sheet and adjust multiregion sheet
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Lines changed: 89 additions & 158 deletions

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‎CHANGELOG.md‎

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@@ -32,6 +32,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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| --RV_primer | --primer_rev | |
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| --classifier | --qiime_classifier | |
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- [#1028](https://github.com/nf-core/ampliseq/pull/1028) - Multi-region sample sheet via `--multiregion` had its header changed from `FW_primer` and `RV_primer` to `primer_fwd` and `primer_rev`, respectively. (by @d4straub)
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### `Fixed`
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- [#1019](https://github.com/nf-core/ampliseq/pull/1019) - Improve channel assignment & improve some version reporting (by @d4straub)
@@ -41,6 +43,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Removed`
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- [#1028](https://github.com/nf-core/ampliseq/pull/1028) - Removed support for the legacy sample sheet to simplify parsing (by @d4straub)
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## nf-core/ampliseq version 2.18.0 - 2026-06-18
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### `Added`

assets/samplesheet_standardized.tsv renamed to assets/samplesheet.tsv

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‎assets/samplesheet_legacy.tsv‎

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‎assets/schema_input.json‎

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"items": {
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"type": "object",
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"properties": {
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"sampleID": {
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"sample": {
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"type": "string",
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"pattern": "^[a-zA-Z][a-zA-Z0-9_]+$",
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"errorMessage": "Unique sample ID must be provided: Must start with a letter, and can only contain letters, numbers or underscores; Regex: '^[a-zA-Z][a-zA-Z0-9_]+$'",
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"meta": ["sample"]
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},
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"forwardReads": {
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"type": "string",
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"format": "file-path",
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"exists": true,
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"pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
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"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
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},
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"reverseReads": {
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"type": "string",
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"format": "file-path",
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"exists": true,
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"pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
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"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
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},
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"sample": {
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"type": "string",
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"pattern": "^[a-zA-Z][a-zA-Z0-9_]+$",
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"errorMessage": "Unique sample ID must be provided: Must start with a letter, and can only contain letters, numbers or underscores; Regex: '^[a-zA-Z][a-zA-Z0-9_]+$'"
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},
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"fastq_1": {
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"type": "string",
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"format": "file-path",
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"meta": ["quant_reading"]
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}
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},
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"oneOf": [
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{
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"required": ["sampleID", "forwardReads"],
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"not": {
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"anyOf": [
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{
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"required": ["sample"]
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},
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{
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"required": ["fastq_1"]
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},
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{
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"required": ["fastq_2"]
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}
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]
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},
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"errorMessage": "When using legacy format (sampleID/forwardReads), do not use standardized fields (sample/fastq_1/fastq_2)"
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},
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{
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"required": ["sample", "fastq_1"],
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"not": {
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"anyOf": [
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{
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"required": ["sampleID"]
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},
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{
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"required": ["forwardReads"]
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},
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{
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"required": ["reverseReads"]
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}
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]
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},
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"errorMessage": "When using standardized format (sample/fastq_1), do not use legacy fields (sampleID/forwardReads/reverseReads)"
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}
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]
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"required": ["sample", "fastq_1"]
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},
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"allOf": [
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{
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"uniqueEntries": ["sample"]
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},
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{
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"uniqueEntries": ["sampleID"]
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}
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]
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"uniqueEntries": ["sample"]
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}

‎assets/schema_multiregion.json‎

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"errorMessage": "Length of region must be an integer",
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"meta": ["region_length"]
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},
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"FW_primer": {
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"primer_fwd": {
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"type": "string",
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"pattern": "^[ATUGCYRSWKMBDHVN]*$",
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"errorMessage": "FW_primer must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
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"errorMessage": "primer_fwd must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
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"meta": ["primer_fwd"]
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},
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"RV_primer": {
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"primer_rev": {
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"type": "string",
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"pattern": "^[ATUGCYRSWKMBDHVN]*$",
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"errorMessage": "RV_primer must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
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"errorMessage": "primer_rev must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
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"meta": ["primer_rev"]
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}
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},
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"required": ["region", "region_length", "FW_primer", "RV_primer"]
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"required": ["region", "region_length", "primer_fwd", "primer_rev"]
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},
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"uniqueEntries": ["region"]
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}

‎conf/test.config‎

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// Input data
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primer_fwd = "GTGYCAGCMGCCGCGGTAA"
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primer_rev = "GGACTACNVGGGTWTCTAAT"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_standardized.tsv"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_v3.tsv"
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metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata.tsv"
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dada_ref_taxonomy = "gtdb=R07-RS207"
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cut_dada_ref_taxonomy = true

‎conf/test_doubleprimers.config‎

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primer_fwd = "NNNNCCTAHGGGRBGCAGCAG"
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primer_rev = "GACTACHVGGGTATCTAATCC"
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double_primer = true
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_double_primer.tsv"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_double_primer_v3.tsv"
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sample_inference = "independent"
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trunc_qmin = 30
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kraken2_ref_taxonomy = "greengenes"

‎conf/test_failed.config‎

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// Input data
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primer_fwd = "GTGYCAGCMGCCGCGGTAA"
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primer_rev = "GGACTACNVGGGTWTCTAAT"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_failed_sample.tsv"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_failed_sample_v3.tsv"
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metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata_failed_sample.tsv"
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sample_inference = "independent"
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dada_ref_tax_custom = "https://zenodo.org/records/4310151/files/rdp_train_set_18.fa.gz"

‎conf/test_full.config‎

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// Input data for full size test
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primer_fwd = "GTGYCAGCMGCCGCGGTAA"
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primer_rev = "GGACTACNVGGGTWTCTAAT"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_full.tsv"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_full_v3.tsv"
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metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata_full.tsv"
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sample_inference = "independent"
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dada_ref_taxonomy = "sbdi-gtdb"

‎conf/test_glosed.config‎

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primer_fwd = "GTGYCAGCMGCCGCGGTAA"
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primer_rev = "GGACTACNVGGGTWTCTAAT"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet.tsv"
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input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_v3.tsv"
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sample_inference = "independent"
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dada_ref_taxonomy = "glosed"
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skip_qiime = true

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