Merge branch 'master' into dev

README.md

@@ -1,9 +1,11 @@
 ![vAMPirus logo](https://raw.githubusercontent.com/Aveglia/vAMPirus/master/example_data/conf/vamplogo.png)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4549851.svg)](https://doi.org/10.5281/zenodo.4549851)
+[![Chat on Gitter](https://img.shields.io/gitter/room/vAMPirusCommunity/Help.svg?colorB=26af64&style=popout)](https://gitter.im/vAMPirusCommunity/Help)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+[![release](https://img.shields.io/github/v/release/Aveglia/vAMPirus?label=release&logo=github)](https://github.com/Aveglia/vAMPirus/releases/latest)
 
 # Table of contents
 * [New in vAMPirus version 2.0.0](#New-in-vAMPirus-version-2.0.0)
@@ -48,7 +50,7 @@ The vAMPirus program contains two different pipelines:
 
 ![vAMPirus DataCheck](https://raw.githubusercontent.com/Aveglia/vAMPirusExamples/main/vampirusflow_datacheckV2.png)
 
-2. Analyze pipeline: a comprehensive analysis of the provided data producing a wide range of results and outputs which includes an interactive report with figures and statistics.
+2. Analyze pipeline: a comprehensive analysis of the provided data producing a wide range of results and outputs which includes an interactive report with figures and statistics. NOTE- stats option has changed on 2/19/21; you only need to add "--stats" to the launch commmand without "run"
 
 
 ![vAMPirus Analyze](https://raw.githubusercontent.com/Aveglia/vAMPirusExamples/main/vampirusflow_analyzeV2.png)
@@ -115,7 +117,11 @@ For more detail see the [manual](https://github.com/Aveglia/vAMPirus/blob/master
 
 Clone the most recent version of vAMPirus from GitHub using:
 
-  git clone https://github.com/Aveglia/vAMPirus.git
+    git clone https://github.com/Aveglia/vAMPirus.git
+
+OR you can download the most recent stable release vAMPirus v1.0.1 (Capsomere I) by using:
+
+    wget https://github.com/Aveglia/vAMPirus/archive/v1.0.1.tar.gz
 
 
 ## Setting up vAMPirus dependencies
@@ -207,11 +213,11 @@ Launch commands for testing (you do not need to edit anything in the config file
 
 ### DataCheck test =>
 
-      `/path/to/nextflow run /path/to/vAMPirus.nf -c /path/to/vampirus.config -profile conda,test --DataCheck`
+      /path/to/nextflow run /path/to/vAMPirus.nf -c /path/to/vampirus.config -profile conda,test --DataCheck
 
 OR
 
-      `nextflow run vAMPirus.nf -c vampirus.config -profile singularity,test --DataCheck`
+      nextflow run vAMPirus.nf -c vampirus.config -profile singularity,test --DataCheck
 
 ### Analyze test =>
 
@@ -236,12 +242,11 @@ Example 1. Launching the vAMPirus DataCheck pipeline using conda and Shannon Ent
 
 Example 2. Launching the vAMPirus DataCheck pipeline using Singularity and multiple primer removal with the path to the fasta file with the primer sequences set in the launch command
 
-      `nextflow run vAMPirus.nf -c vampirus.config -profile singularity --DataCheck --multi --primers /PATH/TO/PRIMERs.fa`
+      nextflow run vAMPirus.nf -c vampirus.config -profile singularity --DataCheck --multi --primers /PATH/TO/PRIMERs.fa
 
 Example 3. Launching the vAMPirus DataCheck pipeline with primer removal by global trimming of 20 bp from forward reads and 26 bp from reverse reads
 
-      `nextflow run vAMPirus.nf -c vampirus.config -profile conda --DataCheck --GlobTrim 20,26`
-
+      nextflow run vAMPirus.nf -c vampirus.config -profile conda --DataCheck --GlobTrim 20,26
 
 ### Analyze pipeline =>
 
@@ -251,13 +256,12 @@ Example 4. Launching the vAMPirus Analyze pipeline with singularity with ASV and
 
 Example 5. Launching the vAMPirus Analyze pipeline with conda to perform multiple primer removal and protein-based clustering of ASVs, but skip most of the extra analyses
 
-      `nextflow run vAMPirus.nf -c vampirus.config -profile conda --Analyze --pcASV --skipPhylogeny --skipEMBOSS --skipTaxonomy --skipReport`
+      nextflow run vAMPirus.nf -c vampirus.config -profile conda --Analyze --pcASV --skipPhylogeny --skipEMBOSS --skipTaxonomy --skipReport
 
 Example 6. Launching vAMPirus Analyze pipeline with conda to produce only ASV and AminoType-based results with Shannon Entropy Analyses with the nodes on produced phylogenies colored based on taxnomy hit
 
       `nextflow run vAMPirus.nf -c vampirus.config -profile conda --Analyze --asvMED --aminoMED --nodeCol TAX --stats`
 
-
 ## Resuming analyses =>
 
 If an analysis is interrupted, you can use Nextflows "-resume" option that will start from the last cached "check point".
@@ -266,12 +270,11 @@ For example if the analysis launched with the command from Example 6 above was i
 
       `nextflow run vAMPirus.nf -c vampirus.config -profile conda --Analyze --asvMED --aminoMED --nodeCol TAX --stats -resume`
 
-
 # Who to cite:
 
 If you do use vAMPirus for your analyses, please cite the following ->
 
-1. vAMPirus - Veglia, A.J., Rivera Vicens, R., Grupstra, C., Howe-Kerr, L., and Correa A.M.S. (2020) vAMPirus: An automated virus amplicon sequencing analysis pipeline. Zenodo. *DOI:*
+1. vAMPirus - Veglia A.J., Rivera Vicéns R.E., Grupstra C.G.B., Howe-Kerr L.I., Correa A.M.S. (2021) vAMPirus: An automated, comprehensive virus amplicon sequencing analysis program (Version v1.0.1). Zenodo. http://doi.org/10.5281/zenodo.4549851
 
 2. DIAMOND - Buchfink B, Xie C, Huson DH. (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods. 12(1):59-60. doi:10.1038/nmeth.3176
 

docs/HelpDocumentation.md

@@ -13,7 +13,7 @@ The vAMPirus program contains two different pipelines:
 
 ![vAMPirus DataCheck](https://raw.githubusercontent.com/Aveglia/vAMPirusExamples/main/vampirusflow_datacheckV2.png)
 
-2. Analyze pipeline: a comprehensive analysis of the provided data producing a wide range of results and outputs which includes an interactive report with figures and statistics.
+2. Analyze pipeline: a comprehensive analysis of the provided data producing a wide range of results and outputs which includes an interactive report with figures and statistics. NOTE- stats option has changed on 2/19/21; you only need to add "--stats" to the launch commmand without "run"
 
 ![vAMPirus Analyze](https://raw.githubusercontent.com/Aveglia/vAMPirusExamples/main/vampirusflow_analyzeV2.png)
 
@@ -1056,6 +1056,7 @@ Here are the options stored within the configuration file:
 
     // ASV filtering parameters - You can set the filtering to run with the command --filter
 
+
         // Path to database containing sequences that if ASVs match to, are then removed prior to any analyses
             filtDB=""
         // Path to database containing sequences that if ASVs match to, are kept for final ASV file to be used in subsequent analyses
@@ -1139,7 +1140,6 @@ Example launch command:
 
           nextflow run vAMPirus.nf -c vampirus.config -profile [conda|singularity] --Analyze --pcASV --clusterAAIDlist .85,.90,.96 --stats
 
-
 ## Minimum Entropy Decomposition (EXPERIMENTAL) - Oligotyping - https://merenlab.org/2012/05/11/oligotyping-pipeline-explained/
 
 In vAMPirus v2, we added the ability for the user to use the oligotyping program employing the Minimum Entropy Decomposition (MED) algorithm developed by Eren et al. 2015 (read more about MED here - https://www.nature.com/articles/ismej2014195#citeas) to cluster ASV or AminoType sequences.
@@ -1186,7 +1186,6 @@ MED related options within the configuration file:
                 aminoC=""
                 aminoSingle=""
 
-
 ## Counts tables and percent ID matrices
 
 vAMPirus generates nucleotide-based counts tables using vsearch and protein-based counts tables using DIAMOND and a custom bash script. Counts tables and percent ID matrices are always produced for each ASV, AminoType and all cASV fasta files produced.
@@ -1208,7 +1207,6 @@ The "--asvcountID" is the percent ID during global alignment that vsearch would
 
 Protein-based counts file generation has a few more parameters the user can alter: "--ProtCountsBit" is the minimum bitscore for an alignment to be recorded, "--ProtCountID" is the minimum percent amino acid similarity an alignment needs to have to be recorded, and "--ProtCountsLength" is the minimum alignment length for a hit to be recorded.
 
-
 ## Phylogenetic analysis and model testing
 
 Phylogenetic trees are produced automatically for ASVs (unless --ncASV specified), ncASVs, pcASVs and aminotypes using IQ-TREE. All produced sequence fastas are aligned using the MAFFT algorithm then alignments are trimmed automatically using TrimAl.
@@ -1222,7 +1220,6 @@ You can tell vAMPirus to color nodes on produced phylogenies based on taxonomy o
 // Color nodes on phylogenetic tree in Analyze report with MED Group information (nodeCol="MED") or taxonomy (nodeCol=TAX) hit. If you would like nodes colored by sequence ID, leave nodeCol="" below.
     nodeCol=""
 
-
 ### Substitution model testing
 
 ModelTest-NG is always ran to determine the best substitution model and all of its output is stored for the users review.
@@ -1711,7 +1708,7 @@ UUsage:
 
   --Statistics options--
 
-        --stats                        Set "--stats run" to signal statstical tests to be performed and included in the final report
+        --stats                        Set "--stats" to signal statstical tests to be performed and included in the final report
 
         --minimumCounts                Minimum number of hit counts for a sample to have to be included in the downstream statistical analyses and report generation
 

vAMPirus.nf

@@ -2967,7 +2967,6 @@ if (params.DataCheck || params.Analyze) {
 
                             elif [ "${params.parametric}" != "false" ];then
                                 iqtree -s \${pre}_Aligned_informativeonly.fasta --prefix \${pre}_iq -m MFP --redo -nt auto -bb ${params.boots} -bnni
-
                             else
                                 iqtree -s \${pre}_Aligned_informativeonly.fasta --prefix \${pre}_iq -m MFP --redo -nt auto -bb ${params.boots} -bnni
                             fi

vampirus.config

@@ -350,6 +350,6 @@ manifest {
     author = 'Alex J. Veglia,Ramón Rivera-Vicéns'
     description = 'Automated virus amplicon sequencing analysis program'
     mainScript = 'vAMPirus.nf'
-    nextflowVersion = '>=20.06.0'
+    nextflowVersion = '>=21.04.1'
     version = '2.0.0'
 }