Merge pull request #96 from Daniel-VM/dev

Prepare release 2.1.0

.github/workflows/awsfulltest.yml

@@ -15,7 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

CHANGELOG.md

@@ -3,44 +3,23 @@
 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).
 
-## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/10/19
+## v2.1.0 nf-core/bacass: "Navy Steel Swordfish" - 2023/10/20
 
-This version implements Bakta for gene annotaton and updates the MultiQC module.
-
-### `Added`
-
-- [#95](https://github.com/nf-core/bacass/pull/95) - Subworkflow for gene annotation with Bakta
-- [#95](https://github.com/nf-core/bacass/pull/95) - Update MultiQC module to v1.17
-
-## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/10/11
-
-Enhancement of the MultiQC report.
-
-### `Added`
-
-- [#93](https://github.com/nf-core/bacass/pull/93) - Add missing modules output to MultiQC.
-
-  - Fastp
-  - PycoQC
-  - Porechop
-  - Quast
-  - Kraken2
-  - Prokka
-
-## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/09/11
-
-This version merges the nf-core template update v2.9. It also updates modules or dependencies to make them work with the new template.
+This version merges the nf-core template updates of v2.9 and v2.10, and updates modules or dependencies to ensure compatibility with the new template. Additionally, new modules have been added to process short-reads and perform gene annotation with Bakta.
 
 ### `Changed`
 
 - [#86](https://github.com/nf-core/bacass/pull/86) - Update nf-core/bacass to the new nf-core 2.9 `TEMPLATE`.
-
 - [#61](https://github.com/nf-core/bacass/issues/61) - Update local/modules to nf-core/modules (detailed below).
+- [#91](https://github.com/nf-core/bacass/pull/91) - Update nf-core/bacass to the new nf-core 2.10 `TEMPLATE`.
+- [#95](https://github.com/nf-core/bacass/pull/95) - Update MultiQC module to v1.17.
 
 ### `Added`
 
-- nf-core subworkflow for trimming and QC of short-reads [nf-core/fastq_trim_fastp_fastqc](https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/fastq_trim_fastp_fastqc).
-- Added parameters: canu_mode, skip_fastqc, skip_fastp
+- [#86](https://github.com/nf-core/bacass/pull/86) - Added nf-core subworkflow for trimming and QC of short-reads [nf-core/fastq_trim_fastp_fastqc](https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/fastq_trim_fastp_fastqc).
+- [#88](https://github.com/nf-core/bacass/pull/88) - Added nf-validation on samplesheet
+- [#93](https://github.com/nf-core/bacass/pull/93) - Added missing modules output to MultiQC. ( Fastp, PycoQC, Porechop, Quast, Kraken2, and Prokka).
+- [#95](https://github.com/nf-core/bacass/pull/95) - Added subworkflow for gene annotation with Bakta.
 
 ### `Fixed`
 

README.md

@@ -48,9 +48,6 @@ to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/i
 with `-profile test` before running the workflow on actual data.
 :::
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):-->
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.tsv`:
@@ -67,23 +64,21 @@ Each row represents a fastq file (single-end) or a pair of fastq files (paired e
 
 Default: Short read assembly with Unicycler, `--kraken2db` can be any [compressed database (`.tar.gz`/`.tgz`)](https://benlangmead.github.io/aws-indexes/k2):
 
-    ```console
-    nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
-    ```
-
-    Long read assembly with Miniasm:
+```console
+nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
+```
 
-    ```console
-    nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --assembly_type 'long' --assembler 'miniasm' --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
-    ```
+Long read assembly with Miniasm:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
+```console
+nextflow run nf-core/bacass -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.tsv --assembly_type 'long' --assembler 'miniasm' --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"
+```
 
 ```bash
 nextflow run nf-core/bacass \
-   -profile <docker/singularity/.../institute> \
-   --input samplesheet.tsv \
-   --outdir <OUTDIR>
+  -profile <docker/singularity/.../institute> \
+  --input samplesheet.tsv \
+  --outdir <OUTDIR>
 ```
 
 :::warning

assets/methods_description_template.yml

@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/bacass Methods Description"
 section_href: "https://github.com/nf-core/bacass"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/dev" target="_blank">nf-core/bacass</a>
+  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/2.1.0" target="_blank">nf-core/bacass</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/bacass/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/bacass/2.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-bacass-methods-description":
     order: -1000

lib/WorkflowBacass.groovy

@@ -49,7 +49,6 @@ class WorkflowBacass {
 
     public static String toolCitationText(params) {
 
-        // TODO nf-core: Optionally add in-text citation tools to this list.
         // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def citation_text = [

nextflow.config

@@ -255,7 +255,7 @@ manifest {
     description     = """Simple bacterial assembly and annotation"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.1.0dev'
+    version         = '2.1.0'
     doi             = '10.5281/zenodo.2669428'
 }