Merge pull request #97 from jfy133/add-taxprofiler

Add taxprofiler support for --nf_core_pipeline

Author: drpatelh

CHANGELOG.md

@@ -7,6 +7,9 @@ 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.
+- Add `enum` field for `--nf_core_pipeline` to parameter schema so only accept supported pipelines are accepted
+
 ## [[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

README.md

@@ -45,7 +45,13 @@ 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)
+- Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
+- [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.
 
 ## Quick Start
 

docs/usage.md

@@ -55,7 +55,13 @@ 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)
+- Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
+- [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. 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`.
 
 ### Bypass `FTP` data download
 

modules/local/sra_to_samplesheet.nf

@@ -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

nextflow_schema.json

@@ -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",