From 2fe3210f88ca8aea591075a7636f1257e644e992 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 09:27:59 -0800
Subject: [PATCH 01/25] Add ivar variants

---
 software/ivar/variants/functions.nf | 59 +++++++++++++++++++++++++++++
 software/ivar/variants/main.nf      | 53 ++++++++++++++++++++++++++
 2 files changed, 112 insertions(+)
 create mode 100644 software/ivar/variants/functions.nf
 create mode 100644 software/ivar/variants/main.nf

diff --git a/software/ivar/variants/functions.nf b/software/ivar/variants/functions.nf
new file mode 100644
index 00000000..d25eea86
--- /dev/null
+++ b/software/ivar/variants/functions.nf
@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
new file mode 100644
index 00000000..93e8d36c
--- /dev/null
+++ b/software/ivar/variants/main.nf
@@ -0,0 +1,53 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process IVAR_VARIANTS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
+
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/1.3.1--h089eab3_0"
+    } else {
+        container "quay.io/biocontainers/1.3.1--h089eab3_0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path fasta
+    path gff_file
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: variants
+    tuple val(meta), path("*.mpileup"), emit: mpileup
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
+    // the gff file is optional, so following the pattern suggested here:
+    //https://github.com/nextflow-io/patterns/blob/master/docs/optional-input.adoc
+    def gff      = gff_file.name != 'NO_FILE' ? "-g $gff_file" : ""
+    """
+    samtools mpileup \\
+        $options.args2 \\
+        --reference $fasta \\
+        $bam | \\
+        $save_mpileup  \\
+        ivar variants \\
+        $options.args \\
+        $gff \\
+        -r $fasta \\
+        -p $prefix
+
+    ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
+    """
+}

From 4ab3ccc9054f19c855f9cef8bdac109c5725a5c3 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 09:28:10 -0800
Subject: [PATCH 02/25] Add ivar variants

---
 .github/filters.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/filters.yml b/.github/filters.yml
index 5a1ed42e..fa37f990 100644
--- a/.github/filters.yml
+++ b/.github/filters.yml
@@ -136,6 +136,10 @@ ivar_trim:
   - software/ivar/trim/**
   - tests/software/ivar/trim/**
 
+ivar_variants:
+  - software/ivar/variants/**
+  - tests/software/ivar/variants/**
+
 minimap2_align:
   - software/minimap2/align/**
   - tests/software/minimap2/align/**

From 9e3c4e598cd48b9d950d47ced301c6d93410aaf0 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 09:29:10 -0800
Subject: [PATCH 03/25] Add meta to ivar variants

---
 software/ivar/variants/meta.yml | 68 +++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 software/ivar/variants/meta.yml

diff --git a/software/ivar/variants/meta.yml b/software/ivar/variants/meta.yml
new file mode 100644
index 00000000..2b815ec1
--- /dev/null
+++ b/software/ivar/variants/meta.yml
@@ -0,0 +1,68 @@
+name: ivar_variants
+description: Call variants from a BAM file using iVar
+keywords:
+    - amplicon sequencing
+    - variants
+    - fasta
+tools:
+    - ivar:
+        description: |
+            iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
+        homepage: https://github.com/andersen-lab/ivar
+        documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file
+        pattern: "*.bam"
+    - fasta:
+        type: file
+        description: The reference sequence used for mapping and generating the BAM file
+        pattern: "*.fa"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - variants:
+        type: file
+        description: iVar generated TSV file with the variants
+        pattern: "*.tsv"
+    - mpileup:
+        type: file
+        description: mpileup output from samtools mpileup [OPTIONAL]
+        pattern: "*.mpileup"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@andersgs"
+    - "@drpatelh"

From 4af7414419f8024e45f967f8cba13e60e24be43a Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 09:29:40 -0800
Subject: [PATCH 04/25] Add tests for ivar variants

---
 tests/data/gff/sarscov2/MN908947.3.gff3 | 27 +++++++++++++++++++++++++
 tests/software/ivar/variants/main.nf    | 25 +++++++++++++++++++++++
 tests/software/ivar/variants/test.yml   | 21 +++++++++++++++++++
 3 files changed, 73 insertions(+)
 create mode 100644 tests/data/gff/sarscov2/MN908947.3.gff3
 create mode 100644 tests/software/ivar/variants/main.nf
 create mode 100644 tests/software/ivar/variants/test.yml

diff --git a/tests/data/gff/sarscov2/MN908947.3.gff3 b/tests/data/gff/sarscov2/MN908947.3.gff3
new file mode 100644
index 00000000..d5cf08a5
--- /dev/null
+++ b/tests/data/gff/sarscov2/MN908947.3.gff3
@@ -0,0 +1,27 @@
+##sequence-region MN908947.3 1 29903
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049
+MN908947.3	Genbank	region	1	29903	.	+	.	ID=MN908947.3:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gb-acronym=SARS-CoV-2;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus
+MN908947.3	Genbank	five_prime_UTR	1	265	.	+	.	ID=id-MN908947.3:1..265;gbkey=5'UTR
+MN908947.3	Genbank	gene	266	21555	.	+	.	ID=gene-orf1ab;Name=orf1ab;gbkey=Gene;gene=orf1ab;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	266	13468	.	+	0	ID=cds-QHD43415.1;Parent=gene-orf1ab;Dbxref=NCBI_GP:QHD43415.1;Name=QHD43415.1;Note=translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=orf1ab;part=1;product=orf1ab polyprotein;protein_id=QHD43415.1
+MN908947.3	Genbank	CDS	13468	21555	.	+	0	ID=cds-QHD43415.1;Parent=gene-orf1ab;Dbxref=NCBI_GP:QHD43415.1;Name=QHD43415.1;Note=translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=orf1ab;part=2;product=orf1ab polyprotein;protein_id=QHD43415.1
+MN908947.3	Genbank	gene	21563	25384	.	+	.	ID=gene-S;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	21563	25384	.	+	0	ID=cds-QHD43416.1;Parent=gene-S;Dbxref=NCBI_GP:QHD43416.1;Name=QHD43416.1;Note=structural protein;gbkey=CDS;gene=S;product=surface glycoprotein;protein_id=QHD43416.1
+MN908947.3	Genbank	gene	25393	26220	.	+	.	ID=gene-ORF3a;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	25393	26220	.	+	0	ID=cds-QHD43417.1;Parent=gene-ORF3a;Dbxref=NCBI_GP:QHD43417.1;Name=QHD43417.1;gbkey=CDS;gene=ORF3a;product=ORF3a protein;protein_id=QHD43417.1
+MN908947.3	Genbank	gene	26245	26472	.	+	.	ID=gene-E;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	26245	26472	.	+	0	ID=cds-QHD43418.1;Parent=gene-E;Dbxref=NCBI_GP:QHD43418.1;Name=QHD43418.1;Note=structural protein%3B E protein;gbkey=CDS;gene=E;product=envelope protein;protein_id=QHD43418.1
+MN908947.3	Genbank	gene	26523	27191	.	+	.	ID=gene-M;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	26523	27191	.	+	0	ID=cds-QHD43419.1;Parent=gene-M;Dbxref=NCBI_GP:QHD43419.1;Name=QHD43419.1;Note=structural protein;gbkey=CDS;gene=M;product=membrane glycoprotein;protein_id=QHD43419.1
+MN908947.3	Genbank	gene	27202	27387	.	+	.	ID=gene-ORF6;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	27202	27387	.	+	0	ID=cds-QHD43420.1;Parent=gene-ORF6;Dbxref=NCBI_GP:QHD43420.1;Name=QHD43420.1;gbkey=CDS;gene=ORF6;product=ORF6 protein;protein_id=QHD43420.1
+MN908947.3	Genbank	gene	27394	27759	.	+	.	ID=gene-ORF7a;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	27394	27759	.	+	0	ID=cds-QHD43421.1;Parent=gene-ORF7a;Dbxref=NCBI_GP:QHD43421.1;Name=QHD43421.1;gbkey=CDS;gene=ORF7a;product=ORF7a protein;protein_id=QHD43421.1
+MN908947.3	Genbank	gene	27894	28259	.	+	.	ID=gene-ORF8;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	27894	28259	.	+	0	ID=cds-QHD43422.1;Parent=gene-ORF8;Dbxref=NCBI_GP:QHD43422.1;Name=QHD43422.1;gbkey=CDS;gene=ORF8;product=ORF8 protein;protein_id=QHD43422.1
+MN908947.3	Genbank	gene	28274	29533	.	+	.	ID=gene-N;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	28274	29533	.	+	0	ID=cds-QHD43423.2;Parent=gene-N;Dbxref=NCBI_GP:QHD43423.2;Name=QHD43423.2;Note=structural protein;gbkey=CDS;gene=N;product=nucleocapsid phosphoprotein;protein_id=QHD43423.2
+MN908947.3	Genbank	gene	29558	29674	.	+	.	ID=gene-ORF10;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding
+MN908947.3	Genbank	CDS	29558	29674	.	+	0	ID=cds-QHI42199.1;Parent=gene-ORF10;Dbxref=NCBI_GP:QHI42199.1;Name=QHI42199.1;gbkey=CDS;gene=ORF10;product=ORF10 protein;protein_id=QHI42199.1
+MN908947.3	Genbank	three_prime_UTR	29675	29903	.	+	.	ID=id-MN908947.3:29675..29903;gbkey=3'UTR
+
diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
new file mode 100644
index 00000000..dca23033
--- /dev/null
+++ b/tests/software/ivar/variants/main.nf
@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+params.save_mpileup = true
+
+include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
+
+workflow test_ivar_variants_no_gff {
+    def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
+    def gff = file('NO_FILE')
+    def input = []
+    input = [ [ id:'test'], 
+                file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
+    IVAR_VARIANTS ( input, ref, gff )
+}
+
+workflow test_ivar_variants_with_gff {
+    def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
+    def gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
+    def input = []
+    input = [ [ id:'test'], 
+                file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
+    IVAR_VARIANTS ( input, ref, gff )
+}
diff --git a/tests/software/ivar/variants/test.yml b/tests/software/ivar/variants/test.yml
new file mode 100644
index 00000000..86f833a6
--- /dev/null
+++ b/tests/software/ivar/variants/test.yml
@@ -0,0 +1,21 @@
+- name: ivar variants no gff
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff -c tests/config/nextflow.config
+  tags:
+    - ivar
+    - ivar_variants
+  files:
+    - path: output/ivar/test.tsv
+      md5sum: 3fd376b8ad80f27a999edf3345d2014a
+    - path: output/ivar/test.mpileup
+      md5sum: b3dfd337dfcd313d6cc9680d7e796fe6
+
+- name: ivar variants with gff
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff -c tests/config/nextflow.config
+  tags:
+    - ivar
+    - ivar_variants
+  files:
+    - path: output/ivar/test.tsv
+      md5sum: 3fd376b8ad80f27a999edf3345d2014a
+    - path: output/ivar/test.mpileup
+      md5sum: b3dfd337dfcd313d6cc9680d7e796fe6
\ No newline at end of file

From e8d1171b5d85768a84397bf478ce182fd83a74ce Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 11:50:52 -0800
Subject: [PATCH 05/25] Make gff a param and not an optional input

---
 software/ivar/variants/main.nf | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index 93e8d36c..71d3bf05 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -22,7 +22,6 @@ process IVAR_VARIANTS {
     input:
     tuple val(meta), path(bam)
     path fasta
-    path gff_file
 
     output:
     tuple val(meta), path("*.tsv"), emit: variants
@@ -32,10 +31,8 @@ process IVAR_VARIANTS {
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
-    // the gff file is optional, so following the pattern suggested here:
-    //https://github.com/nextflow-io/patterns/blob/master/docs/optional-input.adoc
-    def gff      = gff_file.name != 'NO_FILE' ? "-g $gff_file" : ""
+    def save_mpileup = params.containsKey('save_mpileup') ? "tee ${prefix}.mpileup |" : ""
+    def gff      = params.containsKey('gff') ? "-g ${params.get('gff')}" : ""
     """
     samtools mpileup \\
         $options.args2 \\

From 9a5aa0f1452f3dd310df58c4099f73d9d4b4ddb1 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 11:51:04 -0800
Subject: [PATCH 06/25] Fix tests to work with gff param

---
 tests/software/ivar/variants/main.nf | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index dca23033..520cdae1 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -8,18 +8,19 @@ include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addP
 
 workflow test_ivar_variants_no_gff {
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
-    def gff = file('NO_FILE')
     def input = []
     input = [ [ id:'test'], 
                 file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
-    IVAR_VARIANTS ( input, ref, gff )
+    IVAR_VARIANTS ( input, ref )
 }
 
+params.gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
+
 workflow test_ivar_variants_with_gff {
+    
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
-    def gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
     def input = []
     input = [ [ id:'test'], 
                 file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
-    IVAR_VARIANTS ( input, ref, gff )
+    IVAR_VARIANTS ( input, ref )
 }

From f841483a706710f27597f8a2770711f3887d76fa Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 13:23:35 -0800
Subject: [PATCH 07/25] Fix URL for containers

---
 software/ivar/variants/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index 71d3bf05..3ada428e 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -14,9 +14,9 @@ process IVAR_VARIANTS {
     conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
 
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/1.3.1--h089eab3_0"
+        container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
     } else {
-        container "quay.io/biocontainers/1.3.1--h089eab3_0"
+        container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
     }
 
     input:

From ef1e1b25390e4b8515f93d1bf96113db44bc7923 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:51:45 -0800
Subject: [PATCH 08/25] Fix indentation

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/ivar/variants/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index 3ada428e..d285f9c9 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -12,7 +12,6 @@ process IVAR_VARIANTS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
-
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
     } else {

From 6259b7208164d47fe391086e3766a13d6900190d Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:52:30 -0800
Subject: [PATCH 09/25] Fix output format

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/ivar/variants/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index d285f9c9..1777874e 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -23,9 +23,9 @@ process IVAR_VARIANTS {
     path fasta
 
     output:
-    tuple val(meta), path("*.tsv"), emit: variants
-    tuple val(meta), path("*.mpileup"), emit: mpileup
-    path "*.version.txt"          , emit: version
+    tuple val(meta), path("*.tsv")    , emit: tsv
+    tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
+    path "*.version.txt"              , emit: version
 
     script:
     def software = getSoftwareName(task.process)

From 8c483d4c6ab793ce57b2b824e1bd3c4e1048665b Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:53:13 -0800
Subject: [PATCH 10/25] Add gff as input for proper staging

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/ivar/variants/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index 1777874e..6fe755a2 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -20,7 +20,8 @@ process IVAR_VARIANTS {
 
     input:
     tuple val(meta), path(bam)
-    path fasta
+    path  fasta
+    path  gff
 
     output:
     tuple val(meta), path("*.tsv")    , emit: tsv

From 4f8ab8bd6981098802807d31cbcaafeecbffee1f Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:53:30 -0800
Subject: [PATCH 11/25] Rename gff to features

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/ivar/variants/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index 6fe755a2..531db710 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -40,10 +40,10 @@ process IVAR_VARIANTS {
         $bam | \\
         $save_mpileup  \\
         ivar variants \\
-        $options.args \\
-        $gff \\
-        -r $fasta \\
-        -p $prefix
+            $options.args \\
+            $features \\
+            -r $fasta \\
+            -p $prefix
 
     ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
     """

From 8b6989f2d75412a51d368710be968d073fb52e3b Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:54:19 -0800
Subject: [PATCH 12/25] Add gff as input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/software/ivar/variants/main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index 520cdae1..49278623 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -19,8 +19,9 @@ params.gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkI
 workflow test_ivar_variants_with_gff {
     
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
+    def gff = file(params.gff, checkIfExists: true)
     def input = []
     input = [ [ id:'test'], 
-                file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
-    IVAR_VARIANTS ( input, ref )
+              file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
+    IVAR_VARIANTS ( input, ref, gff )
 }

From 39401ccd075c9e27a26b8a395b83fe8128768512 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:54:36 -0800
Subject: [PATCH 13/25] Add gff as input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/software/ivar/variants/main.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index 49278623..d2300e29 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -7,11 +7,12 @@ params.save_mpileup = true
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 
 workflow test_ivar_variants_no_gff {
-    def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
+    def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
+    def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
     def input = []
     input = [ [ id:'test'], 
-                file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
-    IVAR_VARIANTS ( input, ref )
+              file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
+    IVAR_VARIANTS ( input, ref, dummy )
 }
 
 params.gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)

From ee4c2828a0c5ac1faa608e18d3c8dd0e1f35af02 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:55:12 -0800
Subject: [PATCH 14/25] Update gff assignment to string

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/software/ivar/variants/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index d2300e29..f707ae70 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -15,7 +15,7 @@ workflow test_ivar_variants_no_gff {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
-params.gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
+params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
 
 workflow test_ivar_variants_with_gff {
     

From 3188b8e30ec382ccaeb23560f4deb2a6a7928ce7 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:55:34 -0800
Subject: [PATCH 15/25] Add explicit gff is false param

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/software/ivar/variants/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index f707ae70..bc660905 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -3,6 +3,7 @@
 nextflow.enable.dsl = 2
 
 params.save_mpileup = true
+params.gff = false
 
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 

From 26189f41322291c4559c1d10574f257f3a1d643e Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 19:56:22 -0800
Subject: [PATCH 16/25] Change ternary expressions back to traditional format

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/ivar/variants/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf
index 531db710..1f940d67 100644
--- a/software/ivar/variants/main.nf
+++ b/software/ivar/variants/main.nf
@@ -29,10 +29,10 @@ process IVAR_VARIANTS {
     path "*.version.txt"              , emit: version
 
     script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def save_mpileup = params.containsKey('save_mpileup') ? "tee ${prefix}.mpileup |" : ""
-    def gff      = params.containsKey('gff') ? "-g ${params.get('gff')}" : ""
+    def software     = getSoftwareName(task.process)
+    def prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
+    def features     = params.gff ? "-g $gff" : ""
     """
     samtools mpileup \\
         $options.args2 \\

From c12a558f15aa44865490fe946a58f00686d29cfc Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 20:49:27 -0800
Subject: [PATCH 17/25] Add tests without mpileup

---
 tests/software/ivar/variants/main.nf  | 23 ++++++++++++++++++-----
 tests/software/ivar/variants/test.yml | 17 +++++++++++++----
 2 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index bc660905..e1d51c55 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -2,12 +2,12 @@
 
 nextflow.enable.dsl = 2
 
-params.save_mpileup = true
-params.gff = false
-
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 
-workflow test_ivar_variants_no_gff {
+params.save_mpileup = false
+params.gff = false
+
+workflow test_ivar_variants_no_gff_no_mpileup {
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
     def input = []
@@ -16,9 +16,22 @@ workflow test_ivar_variants_no_gff {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
+params.save_mpileup = true
+params.gff = false
+
+workflow test_ivar_variants_no_gff_with_mpileup {
+    def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
+    def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
+    def input = []
+    input = [ [ id:'test'], 
+              file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
+    IVAR_VARIANTS ( input, ref, dummy )
+}
+
+params.save_mpileup = true
 params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
 
-workflow test_ivar_variants_with_gff {
+workflow test_ivar_variants_with_gff_with_mpileup {
     
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def gff = file(params.gff, checkIfExists: true)
diff --git a/tests/software/ivar/variants/test.yml b/tests/software/ivar/variants/test.yml
index 86f833a6..de93c0a3 100644
--- a/tests/software/ivar/variants/test.yml
+++ b/tests/software/ivar/variants/test.yml
@@ -1,5 +1,14 @@
-- name: ivar variants no gff
-  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff -c tests/config/nextflow.config
+- name: ivar variants no gff no mpileup
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c tests/config/nextflow.config
+  tags:
+    - ivar
+    - ivar_variants
+  files:
+    - path: output/ivar/test.tsv
+      md5sum: 3fd376b8ad80f27a999edf3345d2014a
+      
+- name: ivar variants no gff with mpileup
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config
   tags:
     - ivar
     - ivar_variants
@@ -9,8 +18,8 @@
     - path: output/ivar/test.mpileup
       md5sum: b3dfd337dfcd313d6cc9680d7e796fe6
 
-- name: ivar variants with gff
-  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff -c tests/config/nextflow.config
+- name: ivar variants with gff with mpileup
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config
   tags:
     - ivar
     - ivar_variants

From 7cae9b1842c826b4efad237dfa0d4eea1120a422 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 20:49:37 -0800
Subject: [PATCH 18/25] Add gff to meta yaml

---
 software/ivar/variants/meta.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/software/ivar/variants/meta.yml b/software/ivar/variants/meta.yml
index 2b815ec1..6f8e828a 100644
--- a/software/ivar/variants/meta.yml
+++ b/software/ivar/variants/meta.yml
@@ -45,13 +45,17 @@ input:
         type: file
         description: The reference sequence used for mapping and generating the BAM file
         pattern: "*.fa"
+    - gff:
+        type: file
+        description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
+        patter: "*.gff"
 output:
     - meta:
         type: map
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - variants:
+    - tsv:
         type: file
         description: iVar generated TSV file with the variants
         pattern: "*.tsv"

From b99972f3a0f2f1d9d2b63d7c4cf52711570944f9 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 20:59:45 -0800
Subject: [PATCH 19/25] Move params to nextflow invocation

---
 tests/software/ivar/variants/main.nf  | 9 +--------
 tests/software/ivar/variants/test.yml | 4 ++--
 2 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index e1d51c55..ac7e56ed 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -4,9 +4,6 @@ nextflow.enable.dsl = 2
 
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 
-params.save_mpileup = false
-params.gff = false
-
 workflow test_ivar_variants_no_gff_no_mpileup {
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
@@ -16,9 +13,6 @@ workflow test_ivar_variants_no_gff_no_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
-params.save_mpileup = true
-params.gff = false
-
 workflow test_ivar_variants_no_gff_with_mpileup {
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
@@ -28,8 +22,7 @@ workflow test_ivar_variants_no_gff_with_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
-params.save_mpileup = true
-params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
+//params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
 
 workflow test_ivar_variants_with_gff_with_mpileup {
     
diff --git a/tests/software/ivar/variants/test.yml b/tests/software/ivar/variants/test.yml
index de93c0a3..ac78d3d1 100644
--- a/tests/software/ivar/variants/test.yml
+++ b/tests/software/ivar/variants/test.yml
@@ -8,7 +8,7 @@
       md5sum: 3fd376b8ad80f27a999edf3345d2014a
       
 - name: ivar variants no gff with mpileup
-  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config --save_mpileup
   tags:
     - ivar
     - ivar_variants
@@ -19,7 +19,7 @@
       md5sum: b3dfd337dfcd313d6cc9680d7e796fe6
 
 - name: ivar variants with gff with mpileup
-  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup
   tags:
     - ivar
     - ivar_variants

From eeedb959c9e1767ffa20b6ade5b6d0c524f2d5d0 Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Mon, 15 Feb 2021 21:04:17 -0800
Subject: [PATCH 20/25] Clean out comments

---
 tests/software/ivar/variants/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index ac7e56ed..bd5dad80 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -22,8 +22,6 @@ workflow test_ivar_variants_no_gff_with_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
-//params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
-
 workflow test_ivar_variants_with_gff_with_mpileup {
     
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)

From 23987bdad0f2e0adc2a54da68cba5d09a53ef7c7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 16 Feb 2021 22:57:47 +0000
Subject: [PATCH 21/25] Update tests/software/ivar/variants/main.nf

---
 tests/software/ivar/variants/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index bd5dad80..885965eb 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -22,6 +22,8 @@ workflow test_ivar_variants_no_gff_with_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
+params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
+
 workflow test_ivar_variants_with_gff_with_mpileup {
     
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)

From de90d371dc3219aa409b3fa268b9a48d9a4ea18a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 16 Feb 2021 22:58:38 +0000
Subject: [PATCH 22/25] Update tests/software/ivar/variants/main.nf

---
 tests/software/ivar/variants/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index 885965eb..56a61077 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -4,6 +4,8 @@ nextflow.enable.dsl = 2
 
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 
+params.gff = false
+
 workflow test_ivar_variants_no_gff_no_mpileup {
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)

From 27020105aaf50cdb293ff2cce704659b650f3d81 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 16 Feb 2021 23:00:30 +0000
Subject: [PATCH 23/25] Update tests/software/ivar/variants/main.nf

---
 tests/software/ivar/variants/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index 56a61077..56984579 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -4,7 +4,8 @@ nextflow.enable.dsl = 2
 
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 
-params.gff = false
+params.gff          = false
+params.save_mpileup = false
 
 workflow test_ivar_variants_no_gff_no_mpileup {
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)

From 7c276d297422641827f60bfa6d33ee20993c4595 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 16 Feb 2021 23:01:27 +0000
Subject: [PATCH 24/25] Update tests/software/ivar/variants/main.nf

---
 tests/software/ivar/variants/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index 56984579..07999457 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -16,6 +16,9 @@ workflow test_ivar_variants_no_gff_no_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
+params.gff          = false
+params.save_mpileup = true
+
 workflow test_ivar_variants_no_gff_with_mpileup {
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)

From cf2f0762aa44dc822634f11d9db6701b243a6c1e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 16 Feb 2021 23:06:26 +0000
Subject: [PATCH 25/25] Update main.nf

---
 tests/software/ivar/variants/main.nf | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf
index 07999457..306d4585 100644
--- a/tests/software/ivar/variants/main.nf
+++ b/tests/software/ivar/variants/main.nf
@@ -4,10 +4,10 @@ nextflow.enable.dsl = 2
 
 include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
 
-params.gff          = false
-params.save_mpileup = false
-
 workflow test_ivar_variants_no_gff_no_mpileup {
+    params.gff          = false
+    params.save_mpileup = false
+    
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
     def input = []
@@ -16,10 +16,10 @@ workflow test_ivar_variants_no_gff_no_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
-params.gff          = false
-params.save_mpileup = true
-
 workflow test_ivar_variants_no_gff_with_mpileup {
+    params.gff          = false
+    params.save_mpileup = true
+    
     def ref   = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
     def input = []
@@ -28,10 +28,10 @@ workflow test_ivar_variants_no_gff_with_mpileup {
     IVAR_VARIANTS ( input, ref, dummy )
 }
 
-params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
-
 workflow test_ivar_variants_with_gff_with_mpileup {
-    
+    params.gff          = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
+    params.save_mpileup = true
+
     def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
     def gff = file(params.gff, checkIfExists: true)
     def input = []