diff --git a/assets/samplesheet_full.csv b/assets/samplesheet_full.csv
new file mode 100644
index 00000000..36211ac7
--- /dev/null
+++ b/assets/samplesheet_full.csv
@@ -0,0 +1,5 @@
+sample,fastq_1,fastq_2,strandedness
+GM12878,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603629_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603629_T1_2.fastq.gz,reverse
+GM12878,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603630_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603630_T1_2.fastq.gz,reverse
+K562,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603392_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603392_T1_2.fastq.gz,reverse
+K562,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603393_T1_1.fastq.gz,s3://nf-core-awsmegatests/rnaseq/input_data/SRX1603393_T1_2.fastq.gz,reverse
diff --git a/assets/samplesheet_test.csv b/assets/samplesheet_test.csv
index 7131bd5d..fc6dfa21 100644
--- a/assets/samplesheet_test.csv
+++ b/assets/samplesheet_test.csv
@@ -1,2 +1,4 @@
 sample,fastq_1,fastq_2,strandedness
 GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz,reverse
+TEST1,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz,reverse
+TEST2,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz,reverse
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 7634b236..91327e5c 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -1,7 +1,4 @@
-#!/usr/bin/env python
-
-# TODO nf-core: Update the script to check the samplesheet
-# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
+#!/usr/bin/env python3
 
 import os
 import sys
@@ -10,7 +7,7 @@
 
 
 def parse_args(args=None):
-    Description = "Reformat nf-core/rnavar samplesheet file and check its contents."
+    Description = "Reformat nf-core/rnaseq samplesheet file and check its contents."
     Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
@@ -29,63 +26,66 @@ def make_dir(path):
 
 
 def print_error(error, context="Line", context_str=""):
-    error_str = "ERROR: Please check samplesheet -> {}".format(error)
+    error_str = f"ERROR: Please check samplesheet -> {error}"
     if context != "" and context_str != "":
-        error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
-            error, context.strip(), context_str.strip()
-        )
+        error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'"
     print(error_str)
     sys.exit(1)
 
 
-# TODO nf-core: Update the check_samplesheet function
 def check_samplesheet(file_in, file_out):
     """
     This function checks that the samplesheet follows the following structure:
 
-    sample,fastq_1,fastq_2
-    SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz
-    SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz
-    SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,
+    sample,fastq_1,fastq_2,strandedness
+    SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz,forward
+    SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz,forward
+    SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,,forward
 
     For an example see:
-    https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
+    https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv
     """
 
     sample_mapping_dict = {}
-    with open(file_in, "r") as fin:
+    with open(file_in, "r", encoding='utf-8-sig') as fin:
 
         ## Check header
-        MIN_COLS = 2
-        # TODO nf-core: Update the column names for the input samplesheet
-        HEADER = ["sample", "fastq_1", "fastq_2"]
+        MIN_COLS = 3
+        HEADER = ["sample", "fastq_1", "fastq_2", "strandedness"]
         header = [x.strip('"') for x in fin.readline().strip().split(",")]
         if header[: len(HEADER)] != HEADER:
-            print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
+            print(
+                f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}"
+            )
             sys.exit(1)
 
         ## Check sample entries
         for line in fin:
             lspl = [x.strip().strip('"') for x in line.strip().split(",")]
 
-            # Check valid number of columns per row
+            ## Check valid number of columns per row
             if len(lspl) < len(HEADER):
                 print_error(
-                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
+                    f"Invalid number of columns (minimum = {len(HEADER)})!",
                     "Line",
                     line,
                 )
+
             num_cols = len([x for x in lspl if x])
             if num_cols < MIN_COLS:
                 print_error(
-                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
+                    f"Invalid number of populated columns (minimum = {MIN_COLS})!",
                     "Line",
                     line,
                 )
 
             ## Check sample name entries
-            sample, fastq_1, fastq_2 = lspl[: len(HEADER)]
-            sample = sample.replace(" ", "_")
+            sample, fastq_1, fastq_2, strandedness = lspl[: len(HEADER)]
+            if sample.find(" ") != -1:
+                print(
+                    f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
+                )
+                sample = sample.replace(" ", "_")
             if not sample:
                 print_error("Sample entry has not been specified!", "Line", line)
 
@@ -101,16 +101,32 @@ def check_samplesheet(file_in, file_out):
                             line,
                         )
 
+            ## Check strandedness
+            strandednesses = ["unstranded", "forward", "reverse"]
+            if strandedness:
+                if strandedness not in strandednesses:
+                    print_error(
+                        f"Strandedness must be one of '{', '.join(strandednesses)}'!",
+                        "Line",
+                        line,
+                    )
+            else:
+                print_error(
+                    f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
+                    "Line",
+                    line,
+                )
+
             ## Auto-detect paired-end/single-end
-            sample_info = []  ## [single_end, fastq_1, fastq_2]
+            sample_info = []  ## [single_end, fastq_1, fastq_2, strandedness]
             if sample and fastq_1 and fastq_2:  ## Paired-end short reads
-                sample_info = ["0", fastq_1, fastq_2]
+                sample_info = ["0", fastq_1, fastq_2, strandedness]
             elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
-                sample_info = ["1", fastq_1, fastq_2]
+                sample_info = ["1", fastq_1, fastq_2, strandedness]
             else:
                 print_error("Invalid combination of columns provided!", "Line", line)
 
-            ## Create sample mapping dictionary = { sample: [ single_end, fastq_1, fastq_2 ] }
+            ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, strandedness ]]}
             if sample not in sample_mapping_dict:
                 sample_mapping_dict[sample] = [sample_info]
             else:
@@ -124,17 +140,38 @@ def check_samplesheet(file_in, file_out):
         out_dir = os.path.dirname(file_out)
         make_dir(out_dir)
         with open(file_out, "w") as fout:
-            fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
+            fout.write(
+                ",".join(["sample", "single_end", "fastq_1", "fastq_2", "strandedness"])
+                + "\n"
+            )
             for sample in sorted(sample_mapping_dict.keys()):
 
-                ## Check that multiple runs of the same sample are of the same datatype
-                if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
-                    print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
+                ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
+                if not all(
+                    x[0] == sample_mapping_dict[sample][0][0]
+                    for x in sample_mapping_dict[sample]
+                ):
+                    print_error(
+                        f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!",
+                        "Sample",
+                        sample,
+                    )
+
+                ## Check that multiple runs of the same sample are of the same strandedness
+                if not all(
+                    x[-1] == sample_mapping_dict[sample][0][-1]
+                    for x in sample_mapping_dict[sample]
+                ):
+                    print_error(
+                        f"Multiple runs of a sample must have the same strandedness!",
+                        "Sample",
+                        sample,
+                    )
 
                 for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
+                    fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n")
     else:
-        print_error("No entries to process!", "Samplesheet: {}".format(file_in))
+        print_error(f"No entries to process!", "Samplesheet: {file_in}")
 
 
 def main(args=None):
diff --git a/conf/modules.config b/conf/modules.config
index 865c1b44..3c32bd82 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -112,12 +112,19 @@ params {
             publish_dir      = 'variant_calling'
             publish_files    = ['vcf.gz':'', 'vcf.gz.tbi':'']
         }
+        'gatk_indexfeaturefile' {
+            args             = ''
+            suffix           = '.haplotypecaller'
+            publish_by_meta  = true
+            publish_dir      = 'variant_calling'
+            publish_files    = ['vcf.gz':'', 'vcf.gz.tbi':'']
+        }
         'gatk_variantfilter' {
             args             = ''
             suffix           = '.filtered'
             publish_by_meta  = true
             publish_dir      = 'variant_filtering'
-            publish_files    = ['vcf':'', 'vcf.idx':'']
+            publish_files    = ['vcf.gz':'', 'vcf.gz.tbi':'']
         }
         'fastqc' {
             args             = "--quiet"
diff --git a/conf/test.config b/conf/test.config
index c56b48c1..8e85b5ac 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,8 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'assets/samplesheet_test.csv'
+    //input = 'assets/samplesheet_test.csv'
+    input = 'assets/samplesheet_full.csv'
 
     // Genome references
     fasta               = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
diff --git a/modules.json b/modules.json
index 5b2e7d52..c2cfbdf4 100644
--- a/modules.json
+++ b/modules.json
@@ -24,12 +24,21 @@
             "gatk4/createsequencedictionary": {
                 "git_sha": "3b600af50eae8264960df817277cfe303d2acd47"
             },
+            "gatk4/indexfeaturefile": {
+                "git_sha": "1a4c7cec1b9d82fdaa15897d8e9a9e9a4767444d"
+            },
             "gatk4/intervallisttools": {
                 "git_sha": "3b600af50eae8264960df817277cfe303d2acd47"
             },
+            "gatk4/mergevcfs": {
+                "git_sha": "3b600af50eae8264960df817277cfe303d2acd47"
+            },
             "gatk4/splitncigarreads": {
                 "git_sha": "3b600af50eae8264960df817277cfe303d2acd47"
             },
+            "gatk4/variantfiltration": {
+                "git_sha": "3b600af50eae8264960df817277cfe303d2acd47"
+            },
             "gffread": {
                 "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
             },
diff --git a/modules/local/gatk4/applybqsr/functions.nf b/modules/local/gatk4/applybqsr/functions.nf
deleted file mode 100644
index da9da093..00000000
--- a/modules/local/gatk4/applybqsr/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/local/gatk4/applybqsr/main.nf b/modules/local/gatk4/applybqsr/main.nf
deleted file mode 100644
index 8e10a5f2..00000000
--- a/modules/local/gatk4/applybqsr/main.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process GATK4_APPLYBQSR {
-    tag "$meta.id"
-    label 'process_low'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
-
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
-    } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
-    }
-
-    input:
-    tuple val(meta), path(bam), path(bai), path(bqsr_table), path(intervals)
-    path  fasta
-    path  fastaidx
-    path  dict
-
-    output:
-    tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt"          , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def interval = intervals ? "-L ${intervals}" : ""
-    """
-    gatk ApplyBQSR \\
-        -R $fasta \\
-        -I $bam \\
-        --bqsr-recal-file $bqsr_table \\
-        $interval \\
-        -O ${prefix}.bam \\
-        $options.args
-
-    echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
-    """
-}
diff --git a/modules/local/gatk4/applybqsr/meta.yml b/modules/local/gatk4/applybqsr/meta.yml
deleted file mode 100644
index 9bf12f09..00000000
--- a/modules/local/gatk4/applybqsr/meta.yml
+++ /dev/null
@@ -1,58 +0,0 @@
-name: gatk4_applybqsr
-description: Apply base quality score recalibration (BQSR) to a bam file
-keywords:
-  - bqsr
-  - bam
-tools:
-  - gatk4:
-    description: |
-        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
-        with a primary focus on variant discovery and genotyping. Its powerful processing engine
-        and high-performance computing features make it capable of taking on projects of any size.
-    homepage: https://gatk.broadinstitute.org/hc/en-us
-    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
-    doi: 10.1158/1538-7445.AM2017-3590
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: BAM file from alignment
-      pattern: "*.{bam}"
-  - bqsr_table:
-      type: file
-      description: Recalibration table from gatk4_baserecalibrator
-  - fasta:
-      type: file
-      description: The reference fasta file
-  - fastaidx:
-      type: file
-      description: Index of reference fasta file
-  - dict:
-      type: file
-      description: GATK sequence dictionary
-  - intervalsBed:
-      type: file
-      description: Bed file with the genomic regions included in the library (optional)
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-  - bam:
-      type: file
-      description: Recalibrated BAM file
-      pattern: "*.{bam}"
-
-authors:
-  - "@yocra3"
diff --git a/modules/local/gatk4/haplotypecaller/functions.nf b/modules/local/gatk4/haplotypecaller/functions.nf
index da9da093..85628ee0 100644
--- a/modules/local/gatk4/haplotypecaller/functions.nf
+++ b/modules/local/gatk4/haplotypecaller/functions.nf
@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,32 +44,35 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
                 }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
             }
         }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
             }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
         }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
     }
 }
diff --git a/modules/local/gatk4/haplotypecaller/main.nf b/modules/local/gatk4/haplotypecaller/main.nf
index da90ba4b..fc0ee0e9 100644
--- a/modules/local/gatk4/haplotypecaller/main.nf
+++ b/modules/local/gatk4/haplotypecaller/main.nf
@@ -1,21 +1,21 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
 
 process GATK4_HAPLOTYPECALLER {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
@@ -28,33 +28,35 @@ process GATK4_HAPLOTYPECALLER {
     val no_intervals
 
     output:
-    tuple val(meta), path("*.vcf")                , emit: vcf
-    tuple val(meta), path(interval), path("*.vcf"), emit: interval_vcf
-    path "*.version.txt"                          , emit: version
+    tuple val(meta), path("*.vcf.gz")                   , emit: vcf
+    tuple val(meta), path(interval), path("*.vcf.gz")   , emit: interval_vcf
+    path "versions.yml"                                 , emit: versions
 
     script:
-    def software  = getSoftwareName(task.process)
     def prefix    = options.suffix ? "${interval.baseName}_${meta.id}${options.suffix}" : "${interval.baseName}_${meta.id}"
-    def avail_mem = 3
+    def avail_mem       = 3
     if (!task.memory) {
         log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
     } else {
         avail_mem = task.memory.giga
     }
-    def intervalsOptions = no_intervals ? "" : "-L ${interval}"
-    def dbsnpOptions = dbsnp ? "-D ${dbsnp}" : ""
-    //TODO allow ploidy argument here since we allow it for the cnv callers? or is this covered with options? Might unintuitive to use
+    def interval_option = no_intervals ? "" : "-L ${interval}"
+    def dbsnp_option = dbsnp ? "-D ${dbsnp}" : ""
     """
     gatk \\
         --java-options "-Xmx${avail_mem}g" \\
         HaplotypeCaller \\
         -R $fasta \\
         -I $bam \\
-        ${dbsnpOptions} \\
-        ${intervalsOptions} \\
-        -O ${prefix}.vcf \\
-        $options.args
+        ${dbsnp_option} \\
+        ${interval_option} \\
+        -O ${prefix}.vcf.gz \\
+        $options.args \\
+        --tmp-dir .
 
-    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/gatk4/mergevcfs/functions.nf b/modules/local/gatk4/mergevcfs/functions.nf
deleted file mode 100644
index da9da093..00000000
--- a/modules/local/gatk4/mergevcfs/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/local/gatk4/splitncigarreads/functions.nf b/modules/local/gatk4/splitncigarreads/functions.nf
deleted file mode 100644
index da9da093..00000000
--- a/modules/local/gatk4/splitncigarreads/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/local/gatk4/splitncigarreads/meta.yml b/modules/local/gatk4/splitncigarreads/meta.yml
deleted file mode 100644
index e433cbf6..00000000
--- a/modules/local/gatk4/splitncigarreads/meta.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: gatk4_splitncigarreads
-description: Splits reads that contain Ns in their cigar string
-keywords:
-  - vcf
-  - merge
-tools:
-  - gatk4:
-      description: |
-        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
-        with a primary focus on variant discovery and genotyping. Its powerful processing engine
-        and high-performance computing features make it capable of taking on projects of any size.
-      homepage: https://gatk.broadinstitute.org/hc/en-us
-      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
-      doi: 10.1158/1538-7445.AM2017-3590
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test']
-  - bam:
-      type: list
-      description: BAM/SAM/CRAM file containing reads
-      pattern: "*.{bam,sam,cram}"
-  - fasta:
-      type: tuple of files
-      description: |
-        Tuple of fasta file (first), sequence dict (second) and fasta index (third)
-      pattern: ["*.fasta", "*.dict", "*.fai"]
-output:
-  - bam:
-      type: file
-      description: Output file with split reads (BAM/SAM/CRAM)
-      pattern: "*.{bam,sam,cram}"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.version.txt"
-authors:
-  - "@kevinmenden"
diff --git a/modules/local/gatk4/variantfiltration/functions.nf b/modules/local/gatk4/variantfiltration/functions.nf
deleted file mode 100644
index da9da093..00000000
--- a/modules/local/gatk4/variantfiltration/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/nf-core/modules/gatk4/indexfeaturefile/functions.nf b/modules/nf-core/modules/gatk4/indexfeaturefile/functions.nf
new file mode 100644
index 00000000..85628ee0
--- /dev/null
+++ b/modules/nf-core/modules/gatk4/indexfeaturefile/functions.nf
@@ -0,0 +1,78 @@
+//
+//  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()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}
diff --git a/modules/local/gatk4/splitncigarreads/main.nf b/modules/nf-core/modules/gatk4/indexfeaturefile/main.nf
similarity index 52%
rename from modules/local/gatk4/splitncigarreads/main.nf
rename to modules/nf-core/modules/gatk4/indexfeaturefile/main.nf
index d1c328ea..8f40a3e3 100644
--- a/modules/local/gatk4/splitncigarreads/main.nf
+++ b/modules/nf-core/modules/gatk4/indexfeaturefile/main.nf
@@ -1,12 +1,12 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
 
-process GATK4_SPLITNCIGARREADS {
+process GATK4_INDEXFEATUREFILE {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
@@ -19,25 +19,22 @@ process GATK4_SPLITNCIGARREADS {
     }
 
     input:
-    tuple val(meta), path(bam)
-    path(fasta)
-    path(fai)
-    path(dict)
+    tuple val(meta), path(feature_file)
 
     output:
-    tuple val(meta), path('*.bam'), path('*.bai'), emit: bam
-    path  '*.version.txt'                        , emit: version
+    tuple val(meta), path("*.{tbi,idx}"), emit: index
+    path  "versions.yml"                , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-    gatk SplitNCigarReads \\
-        -R $fasta \\
-        -I $bam \\
-        -O ${prefix}.bam \\
-        $options.args
+    gatk \\
+        IndexFeatureFile \\
+        $options.args \\
+        -I $feature_file
 
-    echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/gatk4/indexfeaturefile/meta.yml b/modules/nf-core/modules/gatk4/indexfeaturefile/meta.yml
new file mode 100644
index 00000000..eebe6b85
--- /dev/null
+++ b/modules/nf-core/modules/gatk4/indexfeaturefile/meta.yml
@@ -0,0 +1,42 @@
+name: gatk4_indexfeaturefile
+description: Creates an index for a feature file, e.g. VCF or BED file.
+keywords:
+  - index
+  - feature
+tools:
+  - gatk4:
+      description: Genome Analysis Toolkit (GATK4)
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: "10.1158/1538-7445.AM2017-3590"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - feature_file:
+      type: file
+      description: VCF/BED file
+      pattern: "*.{vcf,vcf.gz,bed,bed.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - index:
+      type: file
+      description: Index for VCF/BED file
+      pattern: "*.{tbi,idx}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@santiagorevale"
diff --git a/modules/nf-core/modules/gatk4/mergevcfs/functions.nf b/modules/nf-core/modules/gatk4/mergevcfs/functions.nf
new file mode 100644
index 00000000..85628ee0
--- /dev/null
+++ b/modules/nf-core/modules/gatk4/mergevcfs/functions.nf
@@ -0,0 +1,78 @@
+//
+//  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()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}
diff --git a/modules/local/gatk4/mergevcfs/main.nf b/modules/nf-core/modules/gatk4/mergevcfs/main.nf
similarity index 66%
rename from modules/local/gatk4/mergevcfs/main.nf
rename to modules/nf-core/modules/gatk4/mergevcfs/main.nf
index 8b9747bc..28073fcb 100644
--- a/modules/local/gatk4/mergevcfs/main.nf
+++ b/modules/nf-core/modules/gatk4/mergevcfs/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -11,11 +11,11 @@ process GATK4_MERGEVCFS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
@@ -24,11 +24,10 @@ process GATK4_MERGEVCFS {
     val   use_ref_dict
 
     output:
-    tuple val(meta), path('*.vcf.gz'), path('*.vcf.gz.tbi'), emit: vcf
-    path  '*.version.txt'                                  , emit: version
+    tuple val(meta), path('*.vcf.gz'), emit: vcf
+    path  "versions.yml"             , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     // Make list of VCFs to merge
@@ -44,6 +43,9 @@ process GATK4_MERGEVCFS {
         $ref \\
         $options.args
 
-    echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/gatk4/mergevcfs/meta.yml b/modules/nf-core/modules/gatk4/mergevcfs/meta.yml
similarity index 90%
rename from modules/local/gatk4/mergevcfs/meta.yml
rename to modules/nf-core/modules/gatk4/mergevcfs/meta.yml
index 14b28fa0..597f9ec6 100644
--- a/modules/local/gatk4/mergevcfs/meta.yml
+++ b/modules/nf-core/modules/gatk4/mergevcfs/meta.yml
@@ -12,6 +12,7 @@ tools:
       homepage: https://gatk.broadinstitute.org/hc/en-us
       documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
       doi: 10.1158/1538-7445.AM2017-3590
+      licence: ['Apache-2.0']
 input:
   - meta:
       type: map
@@ -34,9 +35,9 @@ output:
       type: file
       description: merged vcf file
       pattern: "*.vcf.gz"
-  - version:
+  - versions:
       type: file
-      description: File containing software version
-      pattern: "*.version.txt"
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
   - "@kevinmenden"
diff --git a/modules/nf-core/modules/gatk4/variantfiltration/functions.nf b/modules/nf-core/modules/gatk4/variantfiltration/functions.nf
new file mode 100644
index 00000000..85628ee0
--- /dev/null
+++ b/modules/nf-core/modules/gatk4/variantfiltration/functions.nf
@@ -0,0 +1,78 @@
+//
+//  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()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}
diff --git a/modules/local/gatk4/variantfiltration/main.nf b/modules/nf-core/modules/gatk4/variantfiltration/main.nf
similarity index 56%
rename from modules/local/gatk4/variantfiltration/main.nf
rename to modules/nf-core/modules/gatk4/variantfiltration/main.nf
index d442aba8..c2c7a0b1 100644
--- a/modules/local/gatk4/variantfiltration/main.nf
+++ b/modules/nf-core/modules/gatk4/variantfiltration/main.nf
@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -11,34 +11,36 @@ process GATK4_VARIANTFILTRATION {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
-    tuple val(meta), path(vcf), path (tbi)
+    tuple val(meta), path(vcf), path(vcf_tbi)
     path  fasta
     path  fai
     path  dict
 
     output:
-    tuple val(meta), path("*.vcf"), emit: vcf
-    path "*.version.txt"          , emit: version
-
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    tuple val(meta), path("*.tbi")   , emit: tbi
+    path "versions.yml"              , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     gatk VariantFiltration \\
         -R $fasta \\
         -V $vcf \\
-        -O ${prefix}.vcf \\
+        -O ${prefix}.vcf.gz \\
         $options.args
 
-    echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/gatk4/variantfiltration/meta.yml b/modules/nf-core/modules/gatk4/variantfiltration/meta.yml
similarity index 91%
rename from modules/local/gatk4/variantfiltration/meta.yml
rename to modules/nf-core/modules/gatk4/variantfiltration/meta.yml
index d7f72582..6d4983a6 100644
--- a/modules/local/gatk4/variantfiltration/meta.yml
+++ b/modules/nf-core/modules/gatk4/variantfiltration/meta.yml
@@ -12,6 +12,7 @@ tools:
       homepage: https://gatk.broadinstitute.org/hc/en-us
       documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
       doi: 10.1158/1538-7445.AM2017-3590
+      licence: ['Apache-2.0']
 input:
   - meta:
       type: map
@@ -39,9 +40,9 @@ output:
       type: file
       description: filtered VCF file
       pattern: "*.filtered.{vcf}"
-  - version:
+  - versions:
       type: file
-      description: File containing software version
-      pattern: "*.version.txt"
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
   - "@kevinmenden"
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index c1b07196..7edb4f75 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -26,6 +26,7 @@ workflow INPUT_CHECK {
 def create_fastq_channels(LinkedHashMap row) {
     def meta = [:]
     meta.id           = row.sample
+    meta.sample       = row.sample
     meta.single_end   = row.single_end.toBoolean()
 
     def array = []
diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf
index c930aaa4..1a9cba60 100644
--- a/workflows/rnavar.nf
+++ b/workflows/rnavar.nf
@@ -79,6 +79,7 @@ prepareToolIndices = params.aligner
 
 def publish_genome_options = params.save_reference ? [publish_dir: 'genome']       : [publish_files: false]
 def publish_index_options  = params.save_reference ? [publish_dir: 'genome/index'] : [publish_files: false]
+def untar_options          = [publish_files: false]
 
 if (!params.save_reference) modules['star_genomegenerate']['publish_files'] = false
 
@@ -109,14 +110,16 @@ include { GATK4_BASERECALIBRATOR }  from '../modules/nf-core/modules/gatk4/baser
 include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/modules/gatk4/bedtointervallist/main' addParams(options: modules['gatk_bedtointervallist'])
 include { GATK4_HAPLOTYPECALLER   } from '../modules/local/gatk4/haplotypecaller/main'             addParams(options: modules['gatk_haplotypecaller'])
 include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/modules/gatk4/intervallisttools/main' addParams(options: modules['gatk_intervallisttools'])
-include { GATK4_MERGEVCFS         } from '../modules/local/gatk4/mergevcfs/main'                   addParams(options: modules['gatk_mergevcfs'])
-include { GATK4_VARIANTFILTRATION } from '../modules/local/gatk4/variantfiltration/main'           addParams(options: modules['gatk_variantfilter'])
+include { GATK4_MERGEVCFS         } from '../modules/nf-core/modules/gatk4/mergevcfs/main'         addParams(options: modules['gatk_mergevcfs'])
+include { GATK4_INDEXFEATUREFILE  } from '../modules/nf-core/modules/gatk4/indexfeaturefile/main'  addParams(options: modules['gatk_indexfeaturefile'])
+include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/modules/gatk4/variantfiltration/main' addParams(options: modules['gatk_variantfilter'])
 include { SAMTOOLS_INDEX }          from '../modules/nf-core/modules/samtools/index/main'          addParams(options: modules['samtools_index_genome'])
 
 include { PREPARE_GENOME }          from '../subworkflows/local/prepare_genome'                    addParams(
     genome_options:     publish_genome_options,
     index_options:      publish_index_options,
-    star_index_options: modules['star_genomegenerate']
+    star_index_options: modules['star_genomegenerate'],
+    star_untar_options: untar_options
 )
 include { ALIGN_STAR }              from '../subworkflows/nf-core/align_star'                      addParams(
     align_options: modules['star_align'],
@@ -288,6 +291,73 @@ workflow RNAVAR {
         bam_recalibrated_qc = RECALIBRATE.out.qc
         ch_versions         = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null))
 
+        // MODULE: IntervalListTools from GATK4
+        ch_interval_list_split = Channel.empty()
+
+        if (!params.skip_intervallisttools) {
+            GATK4_INTERVALLISTTOOLS(ch_interval_list)
+            ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten()
+        }
+        else ch_interval_list_split = ch_interval_list
+
+        // MODULE: HaplotypeCaller from GATK4
+        interval_flag = params.no_intervals
+        haplotypecaller_vcf = Channel.empty()
+
+        haplotypecaller_interval_bam = bam_recalibrated.combine(ch_interval_list_split)
+            .map{ meta, bam, bai, interval_list ->
+                new_meta = meta.clone()
+                new_meta.id = meta.id + "_" + interval_list.baseName
+                [new_meta, bam, bai, interval_list]}
+
+        GATK4_HAPLOTYPECALLER(
+            haplotypecaller_interval_bam,
+            params.dbsnp_vcf,
+            params.dbsnp_vcf_index,
+            PREPARE_GENOME.out.dict,
+            PREPARE_GENOME.out.fasta,
+            PREPARE_GENOME.out.fai,
+            interval_flag
+        )
+
+        haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf
+            .map{ meta, vcf ->
+                meta.id = meta.sample
+                [meta, vcf]}
+            .groupTuple()
+
+        ch_versions  = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null))
+        use_ref_dict = true
+
+        GATK4_MERGEVCFS(
+            haplotypecaller_raw,
+            PREPARE_GENOME.out.dict,
+            use_ref_dict
+        )
+        haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf
+        ch_versions  = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null))
+
+        GATK4_INDEXFEATUREFILE(
+            haplotypecaller_vcf
+        )
+        haplotypecaller_vcf_tbi = haplotypecaller_vcf.join(GATK4_INDEXFEATUREFILE.out.index, by: [0])
+        ch_versions  = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null))
+
+        // MODULE: VariantFiltration from GATK4
+        if (!params.skip_variantfiltration) {
+
+            GATK4_VARIANTFILTRATION(
+                haplotypecaller_vcf_tbi,
+                PREPARE_GENOME.out.fasta,
+                PREPARE_GENOME.out.fai,
+                PREPARE_GENOME.out.dict
+            )
+
+            filtered_vcf     = GATK4_VARIANTFILTRATION.out.vcf
+            filtered_vcf_tbi = GATK4_VARIANTFILTRATION.out.tbi
+            ch_versions      = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null))
+        }
+
     }
 
     CUSTOM_DUMPSOFTWAREVERSIONS (