Fix #52

* update docs and README to show how to run Illumina and Nanopore test profiles
* for test_nanopore profile, use updated samplesheet.csv at https://github.com/CFIA-NCFAD/nf-test-datasets/blob/nf-flu/samplesheet/samplesheet_test_nanopore_influenza.csv

CHANGELOG.md

@@ -3,6 +3,13 @@
 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).
 
+## [[3.3.6](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.6)] - 2023-11-01
+
+### Fixes
+
+* docs updated to show proper profile to run test profiles for Illumina and Nanopore locally (#52)
+* `test_nanopore` profile has been updated to run locally with [the test samplesheet.csv updated with URLs to FASTQ files at CFIA-NCFAD/nf-test-datasets](https://github.com/CFIA-NCFAD/nf-test-datasets/blob/nf-flu/samplesheet/samplesheet_test_nanopore_influenza.csv)
+
 ## [[3.3.5](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.5)] - 2023-09-15
 
 ### Fixes

README.md

@@ -32,8 +32,16 @@ After reference sequence selection, the pipeline performs read mapping to each r
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort)_
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
+    For Illumina workflow test:
     ```bash
-    nextflow run CFIA-NCFAD/nf-flu -profile test,<docker/singularity/podman/shifter/charliecloud/conda>
+    nextflow run CFIA-NCFAD/nf-flu -profile test_illumina,<docker/singularity/podman/shifter/charliecloud/conda> \
+      --max_cpus $(nproc) # use all available CPUs; default is 2
+    ```
+
+    For Nanopore workflow test:
+    ```bash
+    nextflow run CFIA-NCFAD/nf-flu -profile test_nanopore,<docker/singularity/podman/shifter/charliecloud/conda> \
+      --max_cpus $(nproc) # use all available CPUs; default is 2
     ```
 
     > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs.

conf/test_nanopore.config

@@ -1,8 +1,10 @@
+// NOTE: For CI, the input samplesheet is specially prepared to test input reads specified as directories containing FASTQ files rather than just links/paths to sample reads.
 params {
-  config_profile_name = 'Test Nanopore Profile'
-  config_profile_description = 'Test pipeline with a real-world influenza virus sequencing; only works with GitHub Actions CI'
+  config_profile_name = 'Nanopore test profile'
+  config_profile_description = 'Test Nanopore workflow'
 
-  // input samplesheet prepared in .github/workflows/ci.yml 
+  input = "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/samplesheet/samplesheet_test_nanopore_influenza.csv"
+  platform = "nanopore"
   max_cpus = 2
   max_memory = 6.GB
   max_time = '1.h'

docs/usage.md

@@ -417,8 +417,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-- `test`
-  - A profile with a complete configuration for automated testing
+- `test_illumina` and `test_nanopore`
+  - Profiles for testing the Illumina and Nanopore workflows, respectively, with complete configuration for automated testing
   - Includes links to test data so needs no other parameters
 
 ### `-resume`

nextflow.config

@@ -63,9 +63,6 @@ params {
 
 includeConfig 'conf/base.config'
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-
 profiles {
   charliecloud {
     charliecloud.enabled   = true
@@ -127,6 +124,9 @@ profiles {
   test_nanopore { includeConfig 'conf/test_nanopore.config' }
 }
 
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
 
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
@@ -151,7 +151,7 @@ manifest {
   description     = 'Influenza A virus genome assembly pipeline'
   homePage        = 'https://github.com/CFIA-NCFAD/nf-flu'
   author          = 'Peter Kruczkiewicz, Hai Nguyen'
-  version         = '3.3.5'
+  version         = '3.3.6'
   nextflowVersion = '!>=22.10.1'
   mainScript      = 'main.nf'
   doi             = '10.5281/zenodo.7011213'