update document and fix nf-core.yml

.nf-core.yml

@@ -1,10 +1,10 @@
 lint:
-  files_exist: false
+  files_exist:
     - assets/nf-core-meta-val_logo_light.png
     - docs/images/nf-core-meta-val_logo_light.png
     - docs/images/nf-core-meta-val_logo_dark.png
     - assets/samplesheet.csv
-  files_unchanged: false
+  files_unchanged:
     - assets/sendmail_template.txt
     - .github/CONTRIBUTING.md
     - .github/ISSUE_TEMPLATE/bug_report.yml

docs/usage.md

@@ -17,7 +17,9 @@ The pipeline, constructed using the `nf-core` [template](https://nf-co.re/tools#
 1. Install Nextflow (>=23.04.0) using the instructions [here.](https://nextflow.io/docs/latest/getstarted.html#installation)
 2. Install one of the following technologies for full pipeline reproducibility: Docker, Singularity, Podman, Shifter or Charliecloud.
 
-## Samplesheet input
+## Input
+
+### Samplesheet
 
 You will need to create a samplesheet in csv format with information about the samples you would like to analyse before running the pipeline. It has to be a comma-separated file and a header row as shown in the examples below.
 
@@ -51,6 +53,22 @@ sample1,run1,ILLUMINA,sample1.unmapped_1.fastq.gz,sample1.unmapped_2.fastq.gz,sa
 sample2,run1,ILLUMINA,sample2.unmapped_1.fastq.gz,sample2.unmapped_2.fastq.gz,sample2.kraken2.kraken2.report.txt,sample2.kraken2.kraken2.classifiedreads.txt,kraken2_kraken2-db.tsv,sample2.centrifuge.txt,sample2.centrifuge.results.txt,centrifuge_centrifuge-db.tsv,sample2.diamond.tsv,diamond_diamond-db.tsv
 ```
 
+### Optional input
+
+#### Pathogen genome database
+
+A concatenated FASTA file containing all the pathogen genomes you are interested in.
+
+#### accession2taxid
+
+A file containing accession IDs of pathogens and their corresponding taxonomic IDs
+
+#### Blastn and/or Blastn database
+
+Use a custom database or download available [NCBI databases](https://ftp.ncbi.nlm.nih.gov/blast/db/). See the [documentation](https://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html). To speed up the BLAST process, it is recommended to use the appropriate database. For example, for viruses, one could use `ref_viruses_rep_genomes` or `refseq_protein` instead of the `nt` or `nr` database.
+
+####
+
 ## Running the pipeline
 
 The example commands for running each workflow are as follows:

nextflow.config

@@ -64,22 +64,22 @@ params {
     validate_params                  = true
 
     // Extract kraken2 reads
-    perform_extract_reads            = false
-    extract_kraken2_reads            = false
-    fastq_output                     = false
-    extract_centrifuge_reads         = false
-    extract_diamond_reads            = false
+    perform_extract_reads               = false
+    extract_kraken2_reads               = false
+    fastq_output                        = false
+    extract_centrifuge_reads            = false
+    extract_diamond_reads               = false
 
     // De novo assembly of extracted taxID reads
     perform_shortread_denovo            = false
     perform_longread_denovo             = false
-    min_read_counts                  = null
-    flye_mode                        = "--nano-corr"
+    min_read_counts                     = null
+    flye_mode                           = "--nano-corr"
 
 
     // Screen pathogens
-    perform_screen_pathogens         = false
-    accession2taxid                  = null
+    perform_screen_pathogens            = false
+    accession2taxid                     = null
 
 
 }