Fix tests

README.md

@@ -156,18 +156,18 @@ For more details and further functionality, please refer to the [usage documenta
 
 An executable Python script called [`fastq_dir_to_samplesheet.py`](https://github.com/nf-core/viralrecon/blob/master/bin/fastq_dir_to_samplesheet.py) has been provided if you are using `--platform illumina` and would like to auto-create an input samplesheet based on a directory containing FastQ files **before** you run the pipeline (requires Python 3 installed locally) e.g.
 
-   ```console
-   wget -L https://raw.githubusercontent.com/nf-core/viralrecon/master/bin/fastq_dir_to_samplesheet.py
-   ./fastq_dir_to_samplesheet.py <FASTQ_DIR> samplesheet.csv
-   ```
+```console
+wget -L https://raw.githubusercontent.com/nf-core/viralrecon/master/bin/fastq_dir_to_samplesheet.py
+./fastq_dir_to_samplesheet.py <FASTQ_DIR> samplesheet.csv
+```
 
 ### Reference genomes
 
 You can find the default keys used to specify `--genome` in the [genomes config file](https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config). This provides default options for
 
-   - Reference genomes (including SARS-CoV-2)
-   - Genome associates primer sets
-   - [Nextclade datasets](https://docs.nextstrain.org/projects/nextclade/en/latest/user/datasets.html)
+- Reference genomes (including SARS-CoV-2)
+- Genome associates primer sets
+- [Nextclade datasets](https://docs.nextstrain.org/projects/nextclade/en/latest/user/datasets.html)
 
 The Pangolin and Nextclade lineage and clade definitions change regularly as new SARS-CoV-2 lineages are discovered. For instructions to use more recent versions of lineage analysis tools like Pangolin and Nextclade please refer to the [updating containers](https://nf-co.re/viralrecon/usage#updating-containers) section in the usage docs.
 

nextflow.config

@@ -112,7 +112,6 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-
 
     // Max resource options
     // Defaults only, expecting to be overwritten

workflows/illumina.nf

@@ -1,3 +1,18 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PRINT PARAMS SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
+
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     VALIDATE INPUTS
@@ -12,8 +27,6 @@ def valid_params = [
     spades_modes      : ['rnaviral', 'corona', 'metaviral', 'meta', 'metaplasmid', 'plasmid', 'isolate', 'rna', 'bio']
 ]
 
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
-
 // Validate input parameters
 WorkflowIllumina.initialise(params, log, valid_params)
 

workflows/nanopore.nf

@@ -1,3 +1,18 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PRINT PARAMS SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
+
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     VALIDATE INPUTS
@@ -9,8 +24,6 @@ def valid_params = [
     artic_minion_aligner : ['minimap2', 'bwa']
 ]
 
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
-
 // Validate input parameters
 WorkflowNanopore.initialise(params, log, valid_params)