diff --git a/CHANGELOG.md b/CHANGELOG.md
index 66753fad..4c614eec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
+
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 
diff --git a/bin/retry_with_backoff.sh b/bin/retry_with_backoff.sh
deleted file mode 100755
index 4bdbf1e0..00000000
--- a/bin/retry_with_backoff.sh
+++ /dev/null
@@ -1,100 +0,0 @@
-#!/usr/bin/env bash
-
-set -u
-
-retry_with_backoff() {
-    local max_attempts=${1}
-    local delay=${2}
-    local max_time=${3}
-    local attempt=1
-    local output=
-    local status=
-
-    shift 3
-
-    while [ ${attempt} -le ${max_attempts} ]; do
-        output=$("${@}")
-        status=${?}
-
-        if [ ${status} -eq 0 ]; then
-            break
-        fi
-
-        if [ ${attempt} -lt ${max_attempts} ]; then
-            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
-            sleep ${delay}
-        elif [ ${attempt} -eq ${max_attempts} ]; then
-            echo "Failed after ${attempt} attempts." >&2
-            return ${status}
-        fi
-
-        attempt=$(( ${attempt} + 1 ))
-        delay=$(( ${delay} * 2 ))
-        if [ ${delay} -ge ${max_time} ]; then
-            delay=${max_time}
-        fi
-    done
-
-    echo "${output}"
-}
-
-RETRY=5
-DELAY=1
-MAX_TIME=60
-
-usage() {
-    echo "Usage:" >&2
-    echo "$(basename ${0}) [-h] [-r NUM] [-d NUM] [-m NUM] COMMAND" >&2
-    echo "Call the given command with retries and exponential backoff." >&2
-    echo "" >&2
-    echo "  -r NUM  Set the number of retry attempts (default ${RETRY})." >&2
-    echo "  -d NUM  Set the base number of seconds to delay (default ${DELAY})." >&2
-    echo "  -m NUM  Set the maximum delay in seconds (default ${MAX_TIME})." >&2
-    echo "" >&2
-}
-
-check_numeric() {
-    local arg=${1}
-    if [[ ! ${arg} =~ ^[0-9]+$ ]]; then
-        echo "Illegal argument: ${arg}" >&2
-        echo "Expected a number." >&2
-        echo "" >&2
-        usage
-        exit 2
-    fi
-}
-
-while getopts ":hr:d:m:" arg; do
-    case ${arg} in
-        h)
-            usage
-            exit 0
-            ;;
-        r)
-            check_numeric ${OPTARG}
-            RETRY=${OPTARG}
-            ;;
-        d)
-            check_numeric ${OPTARG}
-            DELAY=${OPTARG}
-            ;;
-        m)
-            check_numeric ${OPTARG}
-            MAX_TIME=${OPTARG}
-            ;;
-        ?)
-            echo "Invalid option: -${OPTARG}" >&2
-            echo "" >&2
-            usage
-            exit 2
-            ;;
-        :)
-            echo "Missing argument for: -${OPTARG}" >&2
-            echo "" >&2
-            usage
-            exit 2
-            ;;
-    esac
-done
-
-retry_with_backoff ${RETRY} ${DELAY} ${MAX_TIME} ${@:OPTIND}
diff --git a/modules.json b/modules.json
index f39d24ab..fefca2b7 100644
--- a/modules.json
+++ b/modules.json
@@ -5,6 +5,15 @@
         "nf-core/modules": {
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
+            "custom/sratoolsncbisettings": {
+                "git_sha": "b2dbaa99309a2057efc32ef9d029ed91140068df"
+            },
+            "sratools/fasterqdump": {
+                "git_sha": "0cdf7767a79faf424645beeff83ecfa5528b6a7c"
+            },
+            "sratools/prefetch": {
+                "git_sha": "1b228835e9525990db99243cb4f0d07aa6e01bc3"
             }
         }
     }
diff --git a/modules/local/sratools_prefetch.nf b/modules/local/sratools_prefetch.nf
deleted file mode 100644
index 76679a93..00000000
--- a/modules/local/sratools_prefetch.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-
-process SRATOOLS_PREFETCH {
-    tag "$id"
-    label 'process_low'
-    label 'error_retry'
-
-    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
-
-    input:
-    tuple val(meta), val(id)
-
-    output:
-    tuple val(meta), path("$id"), emit: sra
-    path "versions.yml"         , emit: versions
-
-    script:
-    def args = task.ext.args ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-    """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
-
-    retry_with_backoff.sh prefetch \\
-        $args \\
-        --progress \\
-        $id
-
-    vdb-validate $id
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf b/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf
new file mode 100644
index 00000000..21bf3005
--- /dev/null
+++ b/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf
@@ -0,0 +1,20 @@
+process CUSTOM_SRATOOLSNCBISETTINGS {
+    tag 'ncbi-settings'
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+
+    output:
+    path('*.mkfg')     , emit: ncbi_settings
+    path 'versions.yml', emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    shell:
+    config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    template 'detect_ncbi_settings.sh'
+}
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml
new file mode 100644
index 00000000..01e98856
--- /dev/null
+++ b/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml
@@ -0,0 +1,28 @@
+name: "sratoolsncbisettings"
+description: Test for the presence of suitable NCBI settings or create them on the fly.
+keywords:
+  - NCBI
+  - settings
+  - sra-tools
+  - prefetch
+  - fasterq-dump
+tools:
+  - "sratools":
+      description: "SRA Toolkit and SDK from NCBI"
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: "['Public Domain']"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - ncbi_settings:
+      type: file
+      description: An NCBI user settings file.
+      pattern: "*.mkfg"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh b/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
new file mode 100644
index 00000000..cfe3a324
--- /dev/null
+++ b/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+
+set -u
+
+
+# Get the expected NCBI settings path and define the environment variable
+# `NCBI_SETTINGS`.
+eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+
+# If the user settings do not exist yet, create a file suitable for `prefetch`
+# and `fasterq-dump`. If an existing settings file does not contain the required
+# values, error out with a helpful message.
+if [[ ! -f "${NCBI_SETTINGS}" ]]; then
+    printf '!{config}' > 'user-settings.mkfg'
+else
+    prefetch --help &> /dev/null
+    if [[ $? = 78 ]]; then
+        echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
+        "missing the required entries for /LIBS/GUID and"\
+        "/libs/cloud/report_instance_identity."\
+        "Feel free to add the following to your settings file:" >&2
+        echo "$(printf '!{config}')" >&2
+        exit 1
+    fi
+    fasterq-dump --help &> /dev/null
+    if [[ $? = 78 ]]; then
+        echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
+        "missing the required entries for /LIBS/GUID and"\
+        "/libs/cloud/report_instance_identity."\
+        "Feel free to add the following to your settings file:" >&2
+        echo "$(printf '!{config}')" >&2
+        exit 1
+    fi
+    if [[ "${NCBI_SETTINGS}" != *.mkfg ]]; then
+        echo "The detected settings '${NCBI_SETTINGS}' do not have the required"\
+        "file extension '.mkfg'." >&2
+        exit 1
+    fi
+    cp "${NCBI_SETTINGS}" ./
+fi
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(vdb-config --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS
diff --git a/modules/local/sratools_fasterqdump.nf b/modules/nf-core/modules/sratools/fasterqdump/main.nf
similarity index 51%
rename from modules/local/sratools_fasterqdump.nf
rename to modules/nf-core/modules/sratools/fasterqdump/main.nf
index 7a75e551..18f46e51 100644
--- a/modules/local/sratools_fasterqdump.nf
+++ b/modules/nf-core/modules/sratools/fasterqdump/main.nf
@@ -1,4 +1,3 @@
-
 process SRATOOLS_FASTERQDUMP {
     tag "$meta.id"
     label 'process_medium'
@@ -10,27 +9,24 @@ process SRATOOLS_FASTERQDUMP {
 
     input:
     tuple val(meta), path(sra)
+    path ncbi_settings
 
     output:
-    tuple val(meta), path(fastq_output), emit: reads
-    tuple val(meta), path(md5_output)  , emit: md5
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path(output), emit: reads
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args  ?: ''
+    def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
     // for unpaired reads which we ignore here.
-    fastq_output = meta.single_end ? '*.fastq.gz'     : '*_{1,2}.fastq.gz'
-    md5_output = meta.single_end ? '*.fastq.gz.md5' : '*_{1,2}.fastq.gz.md5'
+    output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
+    export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
     fasterq-dump \\
         $args \\
@@ -43,22 +39,6 @@ process SRATOOLS_FASTERQDUMP {
         --processes $task.cpus \\
         *.fastq
 
-    ## Rename FastQ files by meta.id
-    if [ -f  ${sra.name}.fastq.gz ]; then
-        mv ${sra.name}.fastq.gz ${meta.id}.fastq.gz
-        md5sum ${meta.id}.fastq.gz > ${meta.id}.fastq.gz.md5
-    fi
-
-    if [ -f  ${sra.name}_1.fastq.gz ]; then
-        mv ${sra.name}_1.fastq.gz ${meta.id}_1.fastq.gz
-        md5sum ${meta.id}_1.fastq.gz > ${meta.id}_1.fastq.gz.md5
-    fi
-
-    if [ -f  ${sra.name}_2.fastq.gz ]; then
-        mv ${sra.name}_2.fastq.gz ${meta.id}_2.fastq.gz
-        md5sum ${meta.id}_2.fastq.gz > ${meta.id}_2.fastq.gz.md5
-    fi
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
new file mode 100644
index 00000000..d6fbd444
--- /dev/null
+++ b/modules/nf-core/modules/sratools/fasterqdump/meta.yml
@@ -0,0 +1,47 @@
+name: sratools_fasterqdump
+description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - FASTQ
+  - dump
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ["Public Domain"]
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: Directory containing ETL data for the given SRA.
+      pattern: "*/*.sra"
+  - ncbi_settings:
+      type: file
+      description: >
+        An NCBI user settings file.
+      pattern: "*.mkfg"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
new file mode 100644
index 00000000..3426ae12
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/main.nf
@@ -0,0 +1,25 @@
+process SRATOOLS_PREFETCH {
+    tag "$id"
+    label 'process_low'
+
+    conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+
+    input:
+    tuple val(meta), val(id)
+    path ncbi_settings
+
+    output:
+    tuple val(meta), path(id), emit: sra
+    path 'versions.yml'      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    shell:
+    args = task.ext.args ?: ''
+    args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
+    template 'retry_with_backoff.sh'
+}
diff --git a/modules/nf-core/modules/sratools/prefetch/meta.yml b/modules/nf-core/modules/sratools/prefetch/meta.yml
new file mode 100644
index 00000000..a3a26522
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/meta.yml
@@ -0,0 +1,48 @@
+name: sratools_prefetch
+description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
+keywords:
+  - sequencing
+  - fastq
+  - prefetch
+tools:
+  - sratools:
+      description: SRA Toolkit and SDK from NCBI
+      homepage: https://github.com/ncbi/sra-tools
+      documentation: https://github.com/ncbi/sra-tools/wiki
+      tool_dev_url: https://github.com/ncbi/sra-tools
+      licence: ["Public Domain"]
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: val
+      description: >
+        A string denoting an SRA id.
+  - ncbi_settings:
+      type: file
+      description: >
+        An NCBI user settings file.
+      pattern: "*.mkfg"
+
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sra:
+      type: directory
+      description: >
+        Directory containing the ETL data for the given SRA id.
+      pattern: "*/*.sra"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@Midnighter"
diff --git a/modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh b/modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh
new file mode 100644
index 00000000..cec0ab43
--- /dev/null
+++ b/modules/nf-core/modules/sratools/prefetch/templates/retry_with_backoff.sh
@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+
+set -u
+
+retry_with_backoff() {
+    local max_attempts=${1}
+    local delay=${2}
+    local max_time=${3}
+    local attempt=1
+    local output=
+    local status=
+
+    # Remove the first three arguments to this function in order to access
+    # the 'real' command with `${@}`.
+    shift 3
+
+    while [ ${attempt} -le ${max_attempts} ]; do
+        output=$("${@}")
+        status=${?}
+
+        if [ ${status} -eq 0 ]; then
+            break
+        fi
+
+        if [ ${attempt} -lt ${max_attempts} ]; then
+            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
+            sleep ${delay}
+        elif [ ${attempt} -eq ${max_attempts} ]; then
+            echo "Failed after ${attempt} attempts." >&2
+            return ${status}
+        fi
+
+        attempt=$(( ${attempt} + 1 ))
+        delay=$(( ${delay} * 2 ))
+        if [ ${delay} -ge ${max_time} ]; then
+            delay=${max_time}
+        fi
+    done
+
+    echo "${output}"
+}
+
+export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
+
+retry_with_backoff !{args2} \
+    prefetch \
+    !{args} \
+    !{id}
+
+vdb-validate !{id}
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS
diff --git a/subworkflows/local/sra_fastq_sratools.nf b/subworkflows/local/sra_fastq_sratools.nf
deleted file mode 100644
index 1d59eb61..00000000
--- a/subworkflows/local/sra_fastq_sratools.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-//
-// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
-//
-
-include { SRATOOLS_PREFETCH    } from '../../modules/local/sratools_prefetch'
-include { SRATOOLS_FASTERQDUMP } from '../../modules/local/sratools_fasterqdump'
-
-workflow SRA_FASTQ_SRATOOLS {
-    take:
-    sra_ids  // channel: [ val(meta), val(id) ]
-
-    main:
-
-    ch_versions = Channel.empty()
-
-    //
-    // Prefetch sequencing reads in SRA format.
-    //
-    SRATOOLS_PREFETCH ( sra_ids )
-    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
-
-    //
-    // Convert the SRA format into one or more compressed FASTQ files.
-    //
-    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
-    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
-
-    emit:
-    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions                     // channel: [ versions.yml ]
-}
diff --git a/subworkflows/nf-core/srafastq/main.nf b/subworkflows/nf-core/srafastq/main.nf
new file mode 100644
index 00000000..f57b6fac
--- /dev/null
+++ b/subworkflows/nf-core/srafastq/main.nf
@@ -0,0 +1,38 @@
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/nf-core/modules/custom/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/nf-core/modules/sratools/prefetch/main'
+include { SRATOOLS_FASTERQDUMP        } from '../../../modules/nf-core/modules/sratools/fasterqdump/main'
+
+/**
+ * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+ */
+workflow SRAFASTQ {
+    take:
+    sra_ids  // channel: [ val(meta), val(id) ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // Detect existing NCBI user settings or create new ones.
+    //
+    CUSTOM_SRATOOLSNCBISETTINGS()
+    def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings  // value channel: path(settings)
+    ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
+
+    //
+    // Prefetch sequencing reads in SRA format.
+    //
+    SRATOOLS_PREFETCH ( sra_ids, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
+
+    //
+    // Convert the SRA format into one or more compressed FASTQ files.
+    //
+    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
+
+    emit:
+    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/srafastq/meta.yml b/subworkflows/nf-core/srafastq/meta.yml
new file mode 100644
index 00000000..873ccaca
--- /dev/null
+++ b/subworkflows/nf-core/srafastq/meta.yml
@@ -0,0 +1,40 @@
+name: sra_fastq
+description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+keywords:
+  - SRA
+  - NCBI
+  - sequencing
+  - FASTQ
+  - prefetch
+  - fasterq-dump
+modules:
+  - custom/sratoolsncbisettings
+  - sratools/prefetch
+  - sratools/fasterqdump
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - id:
+      type: string
+      description: >
+        SRA run identifier.
+# TODO Update when we decide on a standard for subworkflow docs
+output:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
+      pattern: "*.fastq.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@Midnighter"
diff --git a/workflows/sra.nf b/workflows/sra.nf
index 9336fcc1..2b3cb498 100644
--- a/workflows/sra.nf
+++ b/workflows/sra.nf
@@ -26,7 +26,7 @@ include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
 
-include { SRA_FASTQ_SRATOOLS      } from '../subworkflows/local/sra_fastq_sratools'
+include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
 
 /*
 ========================================================================================
@@ -97,16 +97,16 @@ workflow SRA {
         //
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
-        SRA_FASTQ_SRATOOLS (
+        SRAFASTQ (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
-        ch_versions = ch_versions.mix(SRA_FASTQ_SRATOOLS.out.versions.first())
+        ch_versions = ch_versions.mix(SRAFASTQ.out.versions.first())
 
         //
         // MODULE: Stage FastQ files downloaded by SRA together and auto-create a samplesheet
         //
         SRA_TO_SAMPLESHEET (
-            SRA_FASTQ_FTP.out.fastq.mix(SRA_FASTQ_SRATOOLS.out.reads),
+            SRA_FASTQ_FTP.out.fastq.mix(SRAFASTQ.out.reads),
             params.nf_core_pipeline ?: '',
             params.sample_mapping_fields
         )