diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py
deleted file mode 100755
index ef80ec80..00000000
--- a/bin/sra_runinfo_to_ftp.py
+++ /dev/null
@@ -1,162 +0,0 @@
-#!/usr/bin/env python
-
-
-import argparse
-import csv
-import logging
-import sys
-from itertools import chain
-from pathlib import Path
-
-
-logger = logging.getLogger()
-
-
-def parse_args(args=None):
-    Description = "Create samplesheet with FTP download links and md5ums from sample information obtained via 'sra_ids_to_runinfo.py' script."
-    Epilog = "Example usage: python sra_runinfo_to_ftp.py <FILES_IN> <FILE_OUT>"
-
-    parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
-    parser.add_argument(
-        "files_in",
-        metavar="FILES_IN",
-        help="Comma-separated list of metadata file created from 'sra_ids_to_runinfo.py' script.",
-    )
-    parser.add_argument(
-        "file_out",
-        metavar="FILE_OUT",
-        type=Path,
-        help="Output file containing paths to download FastQ files along with their associated md5sums.",
-    )
-    parser.add_argument(
-        "-l",
-        "--log-level",
-        help="The desired log level (default WARNING).",
-        choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
-        default="WARNING",
-    )
-    return parser.parse_args(args)
-
-
-def valid_fastq_extension(fastq):
-    return fastq.endswith("fastq.gz")
-
-
-def parse_sra_runinfo(file_in):
-    runinfo = {}
-    columns = [
-        "run_accession",
-        "experiment_accession",
-        "library_layout",
-        "fastq_ftp",
-        "fastq_md5",
-    ]
-    extensions = [
-        "fastq_1",
-        "fastq_2",
-        "md5_1",
-        "md5_2",
-        "single_end",
-    ]
-    with open(file_in, "r", newline="") as fin:
-        reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True)
-        header = list(reader.fieldnames)
-        if missing := frozenset(columns).difference(frozenset(header)):
-            logger.critical(f"The following expected columns are missing from {file_in}: " f"{', '.join(missing)}.")
-            sys.exit(1)
-        for row in reader:
-            db_id = row["experiment_accession"]
-            if row["fastq_ftp"]:
-                fq_files = row["fastq_ftp"].split(";")[-2:]
-                fq_md5 = row["fastq_md5"].split(";")[-2:]
-                if len(fq_files) == 1:
-                    assert fq_files[0].endswith(".fastq.gz"), f"Unexpected FastQ file format {file_in.name}."
-                    if row["library_layout"] != "SINGLE":
-                        logger.warning(f"The library layout '{row['library_layout']}' should be " f"'SINGLE'.")
-                    sample = {
-                        "fastq_1": fq_files[0],
-                        "fastq_2": None,
-                        "md5_1": fq_md5[0],
-                        "md5_2": None,
-                        "single_end": "true",
-                    }
-                elif len(fq_files) == 2:
-                    assert fq_files[0].endswith("_1.fastq.gz"), f"Unexpected FastQ file format {file_in.name}."
-                    assert fq_files[1].endswith("_2.fastq.gz"), f"Unexpected FastQ file format {file_in.name}."
-                    if row["library_layout"] != "PAIRED":
-                        logger.warning(f"The library layout '{row['library_layout']}' should be " f"'PAIRED'.")
-                    sample = {
-                        "fastq_1": fq_files[0],
-                        "fastq_2": fq_files[1],
-                        "md5_1": fq_md5[0],
-                        "md5_2": fq_md5[1],
-                        "single_end": "false",
-                    }
-                else:
-                    raise RuntimeError(f"Unexpected number of FastQ files: {fq_files}.")
-            else:
-                # In some instances, FTP links don't exist for FastQ files.
-                # These have to be downloaded with the run accession using sra-tools.
-                sample = dict.fromkeys(extensions, None)
-                if row["library_layout"] == "SINGLE":
-                    sample["single_end"] = "true"
-                elif row["library_layout"] == "PAIRED":
-                    sample["single_end"] = "false"
-
-            sample.update(row)
-            if db_id not in runinfo:
-                runinfo[db_id] = [sample]
-            else:
-                if sample in runinfo[db_id]:
-                    logger.error(
-                        f"Input run info file contains duplicate rows!\n" f"{', '.join([row[col] for col in header])}"
-                    )
-                else:
-                    runinfo[db_id].append(sample)
-
-    return runinfo, header + extensions
-
-
-def sra_runinfo_to_ftp(files_in, file_out):
-    samplesheet = {}
-    header = []
-    for file_in in files_in:
-        runinfo, sample_header = parse_sra_runinfo(file_in)
-        header.append(sample_header)
-        for db_id, rows in runinfo.items():
-            if db_id not in samplesheet:
-                samplesheet[db_id] = rows
-            else:
-                logger.warning(f"Duplicate sample identifier found!\nID: '{db_id}'")
-
-    # Create a combined header from all input files.
-    combined_header = header[0] + list(set().union(chain.from_iterable(header)).difference(header[0]))
-    combined_header.insert(0, "id")
-
-    # Write samplesheet with paths to FastQ files and md5 sums.
-    if samplesheet:
-        with file_out.open("w", newline="") as fout:
-            writer = csv.DictWriter(fout, fieldnames=combined_header, delimiter="\t")
-            writer.writeheader()
-            for db_id in sorted(samplesheet):
-                for idx, row in enumerate(samplesheet[db_id], start=1):
-                    row["id"] = f"{db_id}"
-                    if "run_accession" in row:
-                        row["id"] = f"{db_id}_{row['run_accession']}"
-                    writer.writerow(row)
-
-
-def main(args=None):
-    args = parse_args(args)
-    logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s")
-    files = [Path(x.strip()) for x in args.files_in.split(",")]
-    for path in files:
-        if not path.is_file():
-            logger.critical(f"The given input file {path} was not found!")
-            sys.exit(1)
-    args.file_out.parent.mkdir(parents=True, exist_ok=True)
-    sra_runinfo_to_ftp(files, args.file_out)
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/modules/local/sra_runinfo_to_ftp/main.nf b/modules/local/sra_runinfo_to_ftp/main.nf
index 9c83cf53..181af499 100644
--- a/modules/local/sra_runinfo_to_ftp/main.nf
+++ b/modules/local/sra_runinfo_to_ftp/main.nf
@@ -1,27 +1,131 @@
 
 process SRA_RUNINFO_TO_FTP {
 
-    conda "conda-forge::python=3.9.5"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
-        'biocontainers/python:3.9--1' }"
-
     input:
-    path runinfo
+    path runinfo_file
 
     output:
-    path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: versions
-
-    script:
-    """
-    sra_runinfo_to_ftp.py \\
-        ${runinfo.join(',')} \\
-        ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
-    """
+    path "*.runinfo_ftp.tsv", emit: tsv
+
+    exec:
+    def (runinfo, header) = parseSraRuninfo(runinfo_file)
+    header.add(0, "id")
+
+    def samplesheet = [:]
+    runinfo.each { db_id, rows ->
+        if( db_id !in samplesheet )
+            samplesheet[db_id] = rows
+        else
+            log.warn("Duplicate sample identifier found -- ID: '${db_id}'")
+    }
+
+    def prefix = runinfo_file.name.tokenize(".")[0]
+    def file_out = task.workDir.resolve("${prefix}.runinfo_ftp.tsv")
+    file_out << header.join("\t") << "\n"
+
+    samplesheet
+        .sort { id, _rows -> id }
+        .each { id, rows ->
+            rows.each { row ->
+                row.id = row.run_accession
+                    ? "${id}_${row.run_accession}"
+                    : id
+                def values = header.collect { k -> row[k] }
+                file_out << values.join("\t") << "\n"
+            }
+        }
+}
+
+
+def parseSraRuninfo(file_in) {
+    def runinfo = [:]
+    def columns = [
+        "run_accession",
+        "experiment_accession",
+        "library_layout",
+        "fastq_ftp",
+        "fastq_md5",
+    ]
+    def records = file_in.splitCsv(header: true, sep: "\t")
+    def header = file_in.readLines().first().tokenize("\t")
+    def missing = columns.findAll { c -> c !in header }
+    if( missing )
+        throw new Exception("The following expected columns are missing from ${file_in}: ${missing.join(', ')}.")
+
+    records.each { row ->
+        def db_id = row.experiment_accession
+        def sample = getSample(row, file_in.name)
+
+        sample.putAll(row)
+        if( db_id !in runinfo ) {
+            runinfo[db_id] = [sample]
+        }
+        else {
+            if( sample in runinfo[db_id] )
+                log.error("Input run info file contains duplicate rows: ${row}")
+            else
+                runinfo[db_id].append(sample)
+        }
+    }
+
+    return [ runinfo, (header + getExtensions()).unique() ]
+}
+
+
+def getSample(row, filename) {
+    if( row.fastq_ftp ) {
+        def fq_files = row.fastq_ftp.tokenize(";")
+        def fq_md5 = row.fastq_md5.tokenize(";")
+        if( fq_files.size() == 1 ) {
+            assert fq_files[0].endsWith(".fastq.gz") : "Unexpected FastQ file format ${filename}."
+            if( row.library_layout != "SINGLE" )
+                log.warn("The library layout '${row.library_layout}' should be 'SINGLE'.")
+            return [
+                "fastq_1": fq_files[0],
+                "fastq_2": null,
+                "md5_1": fq_md5[0],
+                "md5_2": null,
+                "single_end": "true",
+            ]
+        }
+
+        if( fq_files.size() == 2 ) {
+            assert fq_files[0].endsWith("_1.fastq.gz") : "Unexpected FastQ file format ${filename}."
+            assert fq_files[1].endsWith("_2.fastq.gz") : "Unexpected FastQ file format ${filename}."
+            if( row.library_layout != "PAIRED" )
+                log.warn("The library layout '${row.library_layout}' should be 'PAIRED'.")
+            return [
+                "fastq_1": fq_files[0],
+                "fastq_2": fq_files[1],
+                "md5_1": fq_md5[0],
+                "md5_2": fq_md5[1],
+                "single_end": "false",
+            ]
+        }
+
+        throw new Exception("Unexpected number of FastQ files: ${fq_files}")
+    }
+
+    // In some instances, FTP links don't exist for FastQ files.
+    // These have to be downloaded with the run accession using sra-tools.
+    def sample = getExtensions().inject([:]) { acc, k ->
+        acc[k] = null
+        acc
+    }
+    if( row.library_layout == "SINGLE" )
+        sample.single_end = "true"
+    else if( row.library_layout == "PAIRED" )
+        sample.single_end = "false"
+    return sample
+}
+
+
+def getExtensions() {
+    return [
+        "fastq_1",
+        "fastq_2",
+        "md5_1",
+        "md5_2",
+        "single_end",
+    ]
 }