Merge pull request #139 from Daniel-VM/dev

Reviewer 2 suggestions before v2.3.0 release

README.md

@@ -50,7 +50,8 @@ In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quas
 
 If Kmerfinder is invoked, the pipeline will group samples according to the [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/)-estimated reference genomes. Afterwards, two QUAST steps will be carried out: an initial ('general') [QUAST](http://bioinf.spbau.ru/quast) of all samples without reference genomes, and subsequently, a 'by reference genome' [QUAST](http://bioinf.spbau.ru/quast) to aggregate samples with their reference genomes.
 
-> NOTE: This scenario is supported when [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) analysis is performed only.
+> [!NOTE]
+> This scenario is supported when [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) analysis is performed only.
 
 ## Usage
 

bin/multiqc_to_custom_csv.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # Sourced and Edited from nf-core/viralrecon:
-#   https://github.com/nf-core/viralrecon/blob/master/bin/multiqc_to_custom_csv.py#L59
+# https://github.com/nf-core/viralrecon/blob/3731dd3a32a67a2648ea22c2bd980c224abdaee2/bin/multiqc_to_custom_csv.py
 import os
 import sys
 import errno

conf/test_full.config

@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_full.tsv'
+    input                       = params.pipelines_testdata_base_path + 'bacass/bacass_full.tsv'
     kraken2db                   = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz'
     kmerfinderdb                = 'https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz'
     ncbi_assembly_metadata      = 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt'

docs/output.md

@@ -255,7 +255,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
   - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
   - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
   - `multiqc_plots/`: directory containing static images from the report in various formats.
-  - summary_assembly_metrics_mqc.csv: custom table containing most relevant assembly QC metrics.
+  - `summary_assembly_metrics_mqc.csv`: custom table containing most relevant assembly QC metrics.
 
 </details>
 

nextflow_schema.json

@@ -83,7 +83,7 @@
                 },
                 "kmerfinderdb": {
                     "type": "string",
-                    "description": "Path to the Kmerfinder bacteria database."
+                    "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz "
                 },
                 "reference_fasta": {
                     "type": "string",
@@ -215,7 +215,7 @@
                 },
                 "skip_kmerfinder": {
                     "type": "boolean",
-                    "description": "Skip contamination analysis with Kmerfinder",
+                    "description": "Skip contamination analysis with [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/)",
                     "fa_icon": "fas fa-forward"
                 },
                 "skip_annotation": {