diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf
index 72314eee..a0928333 100644
--- a/modules/antismash/antismashlitedownloaddatabases/main.nf
+++ b/modules/antismash/antismashlitedownloaddatabases/main.nf
@@ -27,9 +27,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     output:
     path("antismash_db") , emit: database
-    path("css"), emit: css_dir
-    path("detection"), emit: detection_dir
-    path("modules"), emit: modules_dir
+    path("antismash_dir"), emit: antismash_dir
     path "versions.yml", emit: versions
 
     when:
@@ -37,11 +35,19 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     script:
     def args = task.ext.args ?: ''
+    conda = params.enable_conda
     """
     download-antismash-databases \\
         --database-dir antismash_db \\
         $args
 
+    if [[ $conda = false ]]; \
+        then \
+            cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \
+        else \
+            cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml
index 619dc8c2..f7ddf3b0 100644
--- a/modules/antismash/antismashlitedownloaddatabases/meta.yml
+++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml
@@ -50,21 +50,11 @@ output:
       type: directory
       description: Download directory for antiSMASH databases
       pattern: "antismash_db"
-  - css_dir:
+  - antismash_dir:
       type: directory
       description: |
-        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "css"
-  - detection_dir:
-      type: directory
-      description: |
-        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "detection"
-  - modules_dir:
-      type: directory
-      description: |
-        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "modules"
+        antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.
+      pattern: "antismash_dir"
 
 authors:
   - "@jasmezz"
diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index ccd455f4..033186ea 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -10,11 +10,18 @@ process DIAMOND_BLASTP {
     input:
     tuple val(meta), path(fasta)
     path db
-    val outext
+    val out_ext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,7 +29,8 @@ process DIAMOND_BLASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    switch ( outext ) {
+    def columns = blast_columns ? "${blast_columns}" : ''
+    switch ( out_ext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
         case "txt": outfmt = 6; break
@@ -30,6 +38,11 @@ process DIAMOND_BLASTP {
         case "sam": outfmt = 101; break
         case "tsv": outfmt = 102; break
         case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
     }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@@ -39,9 +52,9 @@ process DIAMOND_BLASTP {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
-        --outfmt ${outfmt} \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${outext}
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml
index 1aa36c23..3aa81e53 100644
--- a/modules/diamond/blastp/meta.yml
+++ b/modules/diamond/blastp/meta.yml
@@ -28,7 +28,7 @@ input:
       type: directory
       description: Directory containing the protein blast database
       pattern: "*"
-  - outext:
+  - out_ext:
       type: string
       description: |
         Specify the type of output file to be generated. `blast` corresponds to
@@ -36,12 +36,42 @@ input:
         `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
         taxonomic classification format.
       pattern: "blast|xml|txt|daa|sam|tsv|paf"
+  - blast_columns:
+      type: string
+      description: |
+        Optional space separated list of DIAMOND tabular BLAST output keywords
+        used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
+        DIAMOND documnetation for more information.
 
 output:
-  - txt:
+  - blast:
       type: file
       description: File containing blastp hits
-      pattern: "*.{blastp.txt}"
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
+  - txt:
+      type: file
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 357427eb..d3272279 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -10,11 +10,18 @@ process DIAMOND_BLASTX {
     input:
     tuple val(meta), path(fasta)
     path db
-    val outext
+    val out_ext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,7 +29,8 @@ process DIAMOND_BLASTX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    switch ( outext ) {
+    def columns = blast_columns ? "${blast_columns}" : ''
+    switch ( out_ext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
         case "txt": outfmt = 6; break
@@ -30,6 +38,11 @@ process DIAMOND_BLASTX {
         case "sam": outfmt = 101; break
         case "tsv": outfmt = 102; break
         case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
     }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
@@ -39,9 +52,9 @@ process DIAMOND_BLASTX {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
-        --outfmt ${outfmt} \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${outext}
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 5ee2d55e..2dcd7bc6 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -28,7 +28,7 @@ input:
       type: directory
       description: Directory containing the nucelotide blast database
       pattern: "*"
-  - outext:
+  - out_ext:
       type: string
       description: |
         Specify the type of output file to be generated. `blast` corresponds to
@@ -38,10 +38,34 @@ input:
       pattern: "blast|xml|txt|daa|sam|tsv|paf"
 
 output:
+  - blast:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
   - txt:
       type: file
-      description: File containing blastx hits
-      pattern: "*.{blastx.txt}"
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf
index e8a98156..2650925b 100644
--- a/modules/gatk4/markduplicates/main.nf
+++ b/modules/gatk4/markduplicates/main.nf
@@ -12,7 +12,7 @@ process GATK4_MARKDUPLICATES {
 
     output:
     tuple val(meta), path("*.bam")    , emit: bam
-    tuple val(meta), path("*.bai")    , emit: bai
+    tuple val(meta), path("*.bai")    , optional:true, emit: bai
     tuple val(meta), path("*.metrics"), emit: metrics
     path "versions.yml"               , emit: versions
 
diff --git a/modules/srst2/srst2/main.nf b/modules/srst2/srst2/main.nf
new file mode 100644
index 00000000..e8a91716
--- /dev/null
+++ b/modules/srst2/srst2/main.nf
@@ -0,0 +1,47 @@
+process SRST2_SRST2 {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2':
+        'quay.io/biocontainers/srst2:0.2.0--py27_2'}"
+
+    input:
+    tuple val(meta), path(fastq_s), path(db)
+
+    output:
+    tuple val(meta), path("*_genes_*_results.txt")               , optional:true, emit: gene_results
+    tuple val(meta), path("*_fullgenes_*_results.txt")           , optional:true, emit: fullgene_results
+    tuple val(meta), path("*_mlst_*_results.txt")                , optional:true, emit: mlst_results
+    tuple val(meta), path("*.pileup")                            ,                emit: pileup
+    tuple val(meta), path("*.sorted.bam")                        ,                emit: sorted_bam
+    path "versions.yml"                                          ,                emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def read_s = meta.single_end ? "--input_se ${fastq_s}" : "--input_pe ${fastq_s[0]} ${fastq_s[1]}"
+    if (meta.db=="gene") {
+        database = "--gene_db ${db}"
+    } else if (meta.db=="mlst") {
+        database = "--mlst_db ${db}"
+    } else {
+        error "Please set meta.db to either \"gene\" or \"mlst\""
+    }
+    """
+    srst2 \\
+        ${read_s} \\
+        --threads $task.cpus \\
+        --output ${prefix} \\
+        ${database} \\
+        $args
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/srst2/srst2/meta.yml b/modules/srst2/srst2/meta.yml
new file mode 100644
index 00000000..94c763bb
--- /dev/null
+++ b/modules/srst2/srst2/meta.yml
@@ -0,0 +1,72 @@
+name: srst2_srst2
+description: |
+  Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data,
+  a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc)
+  and report the presence of STs and/or reference genes.
+keywords:
+  - mlst
+  - typing
+  - illumina
+tools:
+  - srst2:
+      description: "Short Read Sequence Typing for Bacterial Pathogens"
+      homepage: "http://katholt.github.io/srst2/"
+      documentation: "https://github.com/katholt/srst2/blob/master/README.md"
+      tool_dev_url: "https://github.com/katholt/srst2"
+      doi: "10.1186/s13073-014-0090-6"
+      licence: ["BSD"]
+
+input:
+  - meta:
+      type: map0.2.0-4
+      description: |
+        Groovy Map containing sample information
+        id: should be the identification number or sample name
+        single_end: should be true for single end data and false for paired in data
+        db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option
+        e.g. [ id:'sample', single_end:false , db:'gene']
+  - fasta:
+      type: file
+      description: |
+        gzipped fasta file. If files are NOT in
+        MiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise
+        default is _1, i.e. expect forward reads as sample_1.fastq.gz).
+      pattern: "*.fastq.gz"
+  - db:
+      type: file
+      description: Database in FASTA format
+      pattern: "*.fasta"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'sample', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - txt:
+      type: file
+      description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing
+      pattern: "*_fullgenes_*_results.txt"
+  - txt:
+      type: file
+      description: A tabulated summary report of samples x genes.
+      pattern: "*_genes_*_results.txt"
+  - txt:
+      type: file
+      description: A tabulated summary report of mlst subtyping.
+      pattern: "*_mlst_*_results.txt"
+  - bam:
+      type: file
+      description: Sorted BAM file
+      pattern: "*.sorted.bam"
+  - pileup:
+      type: file
+      description: SAMtools pileup file
+      pattern: "*.pileup"
+
+authors:
+  - "@jvhagey"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 6e4c36fc..e966f18a 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1775,6 +1775,10 @@ sratools/prefetch:
   - modules/sratools/prefetch/**
   - tests/modules/sratools/prefetch/**
 
+srst2/srst2:
+  - modules/srst2/srst2/**
+  - tests/modules/srst2/srst2/**
+
 ssuissero:
   - modules/ssuissero/**
   - tests/modules/ssuissero/**
diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
index 1079363c..b4a964a0 100644
--- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
+++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
@@ -1,8 +1,8 @@
 - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
   command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
   tags:
-    - antismash
     - antismash/antismashlitedownloaddatabases
+    - antismash
   files:
     - path: output/antismash/versions.yml
       md5sum: 24859c67023abab99de295d3675a24b6
@@ -12,6 +12,5 @@
     - path: output/antismash/antismash_db/pfam
     - path: output/antismash/antismash_db/resfam
     - path: output/antismash/antismash_db/tigrfam
-    - path: output/antismash/css
-    - path: output/antismash/detection
-    - path: output/antismash/modules
+    - path: output/antismash/antismash_dir
+    - path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index 80ea2ec5..ff669233 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -9,18 +9,20 @@ workflow test_diamond_blastp {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    outext = 'txt'
+    out_ext = 'txt'
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
 
 workflow test_diamond_blastp_daa {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    outext = 'daa'
+    out_ext = 'daa'
+    blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index c2b8b6f5..aff4e1c5 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -5,7 +5,6 @@
     - diamond
   files:
     - path: output/diamond/test.diamond_blastp.txt
-      md5sum: 2515cf88590afa32356497e79a51fce9
     - path: output/diamond/versions.yml
 
 - name: diamond blastp test_diamond_blastp_daa
@@ -15,5 +14,4 @@
     - diamond
   files:
     - path: output/diamond/test.diamond_blastp.daa
-      md5sum: 0b539c68a5b66dd6e20ad5d218f4f4c6
     - path: output/diamond/versions.yml
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index d5949762..8316aa91 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,18 +9,20 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    outext = 'txt'
+    out_ext = 'tfdfdt'  // Nonsense file extension to check default case.
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
 
 workflow test_diamond_blastx_daa {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    outext = 'daa'
+    out_ext = 'daa'
+    blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index 9c30ba25..b2b6149f 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -5,7 +5,6 @@
     - diamond/blastx
   files:
     - path: output/diamond/test.diamond_blastx.txt
-      md5sum: eb2aebfa1cb42fcb2121c65528663307
     - path: output/diamond/versions.yml
 
 - name: diamond blastx test_diamond_blastx_daa
diff --git a/tests/modules/srst2/srst2/main.nf b/tests/modules/srst2/srst2/main.nf
new file mode 100644
index 00000000..7d51937b
--- /dev/null
+++ b/tests/modules/srst2/srst2/main.nf
@@ -0,0 +1,53 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf'
+
+workflow test_srst2_srst2_exit {
+
+    input = [
+        [ id:'test', single_end:false, db:"test"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+//        [("")]
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_mlst {
+
+    input = [
+        [ id:'test', single_end:false, db:"mlst"], // meta map
+        [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
+          file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_paired_end {
+
+    input = [
+        [ id:'test', single_end:false, db:"gene"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in tests/config/test_data.config
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_single_end {
+
+    input = [
+        [ id:'test', single_end:true, db:"gene" ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in tests/config/test_data.config
+    ]
+
+    SRST2_SRST2(input)
+}
diff --git a/tests/modules/srst2/srst2/nextflow.config b/tests/modules/srst2/srst2/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/srst2/srst2/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/srst2/srst2/test.yml b/tests/modules/srst2/srst2/test.yml
new file mode 100644
index 00000000..f7621f4f
--- /dev/null
+++ b/tests/modules/srst2/srst2/test.yml
@@ -0,0 +1,51 @@
+- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  exit_code: 1
+
+- name: srst2 srst2 test_srst2_srst2_mlst
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__SRR9067271.MLST_DB.pileup
+      contains:
+        - "dnaJ-1	2	C	17	.........,.......	FFFFFFFFFFFFFFFFF"
+    - path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
+    - path: output/srst2/test__mlst__MLST_DB__results.txt
+      md5sum: ec1b1f69933401d67c57f64cad11a098
+    - path: output/srst2/versions.yml
+      md5sum: a0c256a2fd3636069710b8ef22ee5ea7
+
+- name: srst2 srst2 test_srst2_srst2_paired_end
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
+      md5sum: 099aa6cacec5524b311f606debdfb3a9
+    - path: output/srst2/test__test1.resFinder_20180221_srst2.pileup
+      md5sum: 64b512ff495b828c456405ec7b676ad1
+    - path: output/srst2/test__test1.resFinder_20180221_srst2.sorted.bam
+    - path: output/srst2/versions.yml
+      md5sum: b446a70f1a2b4f60757829bcd744a214
+
+- name: srst2 srst2 test_srst2_srst2_single_end
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
+      md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
+    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
+      md5sum: b8850c6644406d8b131e471ecc3f9013
+    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.pileup
+      md5sum: 5f6279dc8124aa762a9dfe3d7a871277
+    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
+    - path: output/srst2/versions.yml
+      md5sum: 790fe00493c6634d17801a930073218b