From 75b99736fc9790de030353611c2f5b991dc05af0 Mon Sep 17 00:00:00 2001
From: Khi Pin <khipinchua@gmail.com>
Date: Tue, 26 Jul 2022 18:17:26 -0700
Subject: [PATCH] Added version to pipeline

---
 README.md | 1 +
 main.nf   | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/README.md b/README.md
index 99dafea..3507684 100644
--- a/README.md
+++ b/README.md
@@ -121,6 +121,7 @@ nextflow run main.nf --help
   --download_db    Download databases needed for taxonomy classification only. Will not
                    run the pipeline. Databases will be downloaded to a folder "databases"
                    in the Nextflow pipeline directory.
+  --version    Output version
 ```
 
 To test the pipeline, run the example below. Note that the path of the database needs
diff --git a/main.nf b/main.nf
index 6aca67e..81806db 100644
--- a/main.nf
+++ b/main.nf
@@ -73,12 +73,16 @@ def helpMessage() {
   --download_db    Download databases needed for taxonomy classification only. Will not
                    run the pipeline. Databases will be downloaded to a folder "databases"
                    in the Nextflow pipeline directory.
+  --version    Output version
   """
 }
 
 // Show help message
 params.help = false
 if (params.help) exit 0, helpMessage()
+params.version = false
+version = "0.2"
+if (params.version) exit 0, log.info("$version")
 params.download_db = false
 params.skip_primer_trim = false
 params.filterQ = 20
@@ -149,6 +153,7 @@ log.info """
   Minimum amplicon length filtered in DADA2: $params.min_len
   Maximum amplicon length filtered in DADA2: $params.max_len
   maxEE parameter for DADA2 filterAndTrim: $params.max_ee
+  minQ parameter for DADA2 filterAndTrim: $params.minQ
   Pooling method for DADA2 denoise process: $params.pooling_method
   Minimum number of samples required to keep any ASV: $params.min_asv_sample
   Minimum number of reads required to keep any ASV: $params.min_asv_totalfreq 
@@ -166,6 +171,7 @@ log.info """
   Number of threads specified for VSEARCH: $params.vsearch_cpu
   Script location for HTML report generation: $params.rmd_vis_biom_script
   Container enabled via docker/singularity: $params.enable_container
+  Version of Nextflow pipeline: $version
 """
 
 // QC before cutadapt