Merge pull request #1027 from d4straub/update-params

Adjust parameter naming and add parameter types

Author: d4straub

.github/workflows/nf-test.yml

@@ -9,7 +9,7 @@ on:
       - "**/*.svg"
   release:
     types: [published]
-  workflow_dispatch:
+  workflow_dispatch: null
 
 # Cancel if a newer run is started
 concurrency:
@@ -50,7 +50,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 17
+          max_shards: 18
 
       - name: debug
         run: |
@@ -79,8 +79,8 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.10.4"
-          - "latest-everything"
+          - 26.04.0
+          - latest-everything
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}

.nf-core.yml

@@ -1,4 +1,6 @@
 lint:
+  nextflow_config: false # TODO: Remove when tools supports parameter types
+  schema_params: false # TODO: Remove when tools supports parameter types
   files_exist:
     - conf/igenomes.config
   files_unchanged:
@@ -8,11 +10,11 @@ lint:
     - assets/nf-core-ampliseq_logo_dark.png
     - docs/images/nf-core-ampliseq_logo_light.png
     - docs/images/nf-core-ampliseq_logo_dark.png
-  nextflow_config:
-    - config_defaults:
-        - params.report_template
-        - params.report_css
-        - params.report_logo
+#  nextflow_config: # TODO: Enable when tools supports parameter types
+#    - config_defaults:
+#        - params.report_template
+#        - params.report_css
+#        - params.report_logo
 nf_core_version: 4.0.2
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## nf-core/ampliseq version 2.19.0dev - [YYYY-MM-DD]
+## nf-core/ampliseq version 3.0.0dev - [YYYY-MM-DD]
 
 ### `Added`
 
@@ -14,10 +14,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#1018](https://github.com/nf-core/ampliseq/pull/1018) - Change version to 2.19.0dev (by @d4straub)
+- [#1027](https://github.com/nf-core/ampliseq/pull/1027) - Changed parameters, including the default of `--sample_inference` from `independent` to `pooled` and `--dada_taxonomy_rc` isnt enforced with IonTorrent and PacBio any more (by @d4straub)
+
+| previously        | now                           | comment |
+| ----------------- | ----------------------------- | ------- |
+| --nanopore        | --sequencing_type nanopore    |         |
+| --pacbio          | --sequencing_type pacbio      |         |
+| --iontorrent      | --sequencing_type nanopore    |         |
+| --single_end      | --sequencing_type illumina_se |         |
+| default           | --sequencing_type illumina_pe | default |
+|                   | --asv_calling auto            | default |
+| default           | --asv_calling dada2           | new     |
+|                   | --asv_calling savont          | new     |
+| --illumina_pe_its | --illumina_pe_readthrough     |         |
+| --extension       | --input_folder_extensions     |         |
+| --FW_primer       | --primer_fwd                  |         |
+| --RV_primer       | --primer_rev                  |         |
+| --classifier      | --qiime_classifier            |         |
 
 ### `Fixed`
 
 - [#1019](https://github.com/nf-core/ampliseq/pull/1019) - Improve channel assignment & improve some version reporting (by @d4straub)
+- [#1027](https://github.com/nf-core/ampliseq/pull/1027) - SBDI's file `dna.tsv` recorded "paired" as lib_layout if `--single_end` was not specified alongside `--pacbio` or `--iontorrent`; now reports "single" in that cases (by @d4straub)
 
 ### `Dependencies`
 

README.md

@@ -11,7 +11,7 @@
 
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1493841-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1493841)[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-important?labelColor=000000)](https://doi.org/10.3389/fmicb.2020.550420)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -66,8 +66,8 @@ Now, you can run the pipeline using:
 nextflow run nf-core/ampliseq \
    -profile <docker/singularity/.../institute> \
    --input "samplesheet.tsv" \
-   --FW_primer "GTGYCAGCMGCCGCGGTAA" \
-   --RV_primer "GGACTACNVGGGTWTCTAAT" \
+   --primer_fwd "GTGYCAGCMGCCGCGGTAA" \
+   --primer_rev "GGACTACNVGGGTWTCTAAT" \
    --outdir <OUTDIR>
 ```
 

assets/schema_multiregion.json

@@ -22,13 +22,13 @@
                 "type": "string",
                 "pattern": "^[ATUGCYRSWKMBDHVN]*$",
                 "errorMessage": "FW_primer must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
-                "meta": ["fw_primer"]
+                "meta": ["primer_fwd"]
             },
             "RV_primer": {
                 "type": "string",
                 "pattern": "^[ATUGCYRSWKMBDHVN]*$",
                 "errorMessage": "RV_primer must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
-                "meta": ["rv_primer"]
+                "meta": ["primer_rev"]
             }
         },
         "required": ["region", "region_length", "FW_primer", "RV_primer"]