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Add taxprofiler support for --nf_core_pipeline #97

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Jun 30, 2022
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Add taxprofiler support for --nf_core_pipeline #97

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ca314f0
Add taxprofiler to pipeline and add enum for --nf_core_pipeline
jfy133 Jun 11, 2022
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Update changelog and docs
jfy133 Jun 11, 2022
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jfy133 Jun 11, 2022
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jfy133 Jun 11, 2022
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [#97](https://github.com/nf-core/fetchngs/pull/97) - Add support for generating nf-core/taxprofiler compatible samplesheets anda dded improved validation for the --nf_core_pipeline flag to only accept supported pipelines
-
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### Enhancements & fixes

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## [[1.6](https://github.com/nf-core/fetchngs/releases/tag/1.6)] - 2022-05-17

- [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -45,7 +45,7 @@ Via a single file of ids, provided one-per-line (see [example input file](https:

### Samplesheet format

The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format), as well as [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
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## Quick Start

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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -55,7 +55,7 @@ The final sample information for the FastQ files used for samplesheet generation

### Samplesheet format

As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
As a bonus, the columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input) and the Illumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format) as well [nf-core/taxprofiler](https://nf-co.re/taxprofiler/usage#samplesheet-input). You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core. It is highly recommended that you double-check that all of the identifiers you defined using `--input` are represented in the samplesheet. Also, public databases don't reliably hold information such as strandedness information so you may need to amend these entries too if for example your samplesheet was created by providing `--nf_core_pipeline rnaseq`.
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### Bypass `FTP` data download

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2 changes: 2 additions & 0 deletions modules/local/sra_to_samplesheet.nf
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Expand Up @@ -39,6 +39,8 @@ process SRA_TO_SAMPLESHEET {
if (pipeline) {
if (pipeline == 'rnaseq') {
pipeline_map << [ strandedness: 'unstranded' ]
} else if (pipeline == 'taxprofiler') {
pipeline_map << [ fasta: '' ]
}
}
pipeline_map << meta_map
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3 changes: 2 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -43,7 +43,8 @@
"nf_core_pipeline": {
"type": "string",
"fa_icon": "fab fa-apple",
"description": "Name of supported nf-core pipeline e.g. 'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns."
"description": "Name of supported nf-core pipeline e.g. 'rnaseq'. A samplesheet for direct use with the pipeline will be created with the appropriate columns.",
"enum": ["rnaseq", "viralrecon", "taxprofiler"]
},
"force_sratools_download": {
"type": "boolean",
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