diff --git a/samtools-stats/.dockerignore b/samtools-stats/.dockerignore
new file mode 100644
index 0000000..71266ec
--- /dev/null
+++ b/samtools-stats/.dockerignore
@@ -0,0 +1,5 @@
+.gitignore
+.nextflow*
+tests
+work
+outdir
diff --git a/samtools-stats/Dockerfile b/samtools-stats/Dockerfile
new file mode 100644
index 0000000..50a9faf
--- /dev/null
+++ b/samtools-stats/Dockerfile
@@ -0,0 +1,32 @@
+FROM ubuntu:20.04
+
+LABEL org.opencontainers.image.source https://github.com/icgc-argo-qc-wg/argo-qc-tools
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update -y && \
+    apt-get install -y software-properties-common python3-pip python3-dev curl && \
+    apt-get install -y libz-dev pkg-config libtool m4 autotools-dev automake libncurses5-dev libbz2-dev liblzma-dev
+
+# install samtools 1.12
+RUN cd /tmp \
+    && curl -sSL -o samtools-1.12.tar.bz2 --retry 10 https://github.com/samtools/samtools/releases/download/1.12/samtools-1.12.tar.bz2 \
+    && bunzip2 -c samtools-1.12.tar.bz2 |tar xf - \
+    && cd samtools-1.12 \
+    && ./configure --prefix=/usr/local \
+    && make \
+    && make install
+
+ENV PATH="/tools:${PATH}"
+
+COPY *.py /tools/
+
+RUN groupadd -g 1000 ubuntu && \
+    useradd -l -u 1000 -g ubuntu ubuntu && \
+    install -d -m 0755 -o ubuntu -g ubuntu /home/ubuntu
+
+USER ubuntu
+
+ENTRYPOINT ["/usr/bin/env"]
+
+CMD ["/bin/bash"]
diff --git a/samtools-stats/main.nf b/samtools-stats/main.nf
new file mode 100755
index 0000000..55e9bf2
--- /dev/null
+++ b/samtools-stats/main.nf
@@ -0,0 +1,91 @@
+#!/usr/bin/env nextflow
+
+/*
+  Copyright (c) 2021, ICGC ARGO
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+  Authors:
+    Junjun Zhang
+*/
+
+/********************************************************************/
+/* this block is auto-generated based on info from pkg.json where   */
+/* changes can be made if needed, do NOT modify this block manually */
+nextflow.enable.dsl = 2
+version = '0.1.0'  // package version
+
+container = [
+    'ghcr.io': 'ghcr.io/icgc-argo-qc-wg/argo-qc-tools.samtools-stats'
+]
+default_container_registry = 'ghcr.io'
+/********************************************************************/
+
+
+// universal params go here
+params.container_registry = ""
+params.container_version = ""
+params.container = ""
+
+params.cpus = 1
+params.mem = 1  // GB
+params.publish_dir = ""  // set to empty string will disable publishDir
+
+// tool specific parmas go here, add / change as needed
+params.aligned_seq = ""
+params.ref_genome_gz = ""  // reference genome: *.fa.gz, index file: *.fa.gz.fai
+
+
+include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/main.nf'
+
+process samtoolsStats {
+  container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
+  publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir
+
+  cpus params.cpus
+  memory "${params.mem} GB"
+
+  input:
+    path aligned_seq
+    path ref_genome_gz
+    path ref_genome_gz_idx
+
+  output:
+    path "${aligned_seq}.samtools_stats.qc.tgz", emit: qc_tar
+
+  script:
+    """
+    main.py -s ${aligned_seq} \
+            -r ${ref_genome_gz} \
+            -t ${params.cpus}
+    """
+}
+
+
+// this provides an entry point for this main script, so it can be run directly without clone the repo
+// using this command: nextflow run <git_acc>/<repo>/<pkg_name>/<main_script>.nf -r <pkg_name>.v<pkg_version> --params-file xxx
+workflow {
+  samtoolsStats(
+    file(params.aligned_seq),
+    file(params.ref_genome_gz),
+    Channel.fromPath(
+      getSecondaryFiles(params.ref_genome_gz, ['fai']), checkIfExists: true
+    ).collect()
+  )
+}
diff --git a/samtools-stats/main.py b/samtools-stats/main.py
new file mode 100755
index 0000000..df3d623
--- /dev/null
+++ b/samtools-stats/main.py
@@ -0,0 +1,176 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+  Copyright (c) 2021, ICGC ARGO
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+  Authors:
+    Junjun Zhang
+"""
+
+import os
+import sys
+import argparse
+import subprocess
+from multiprocessing import cpu_count
+from glob import glob
+import json
+import tarfile
+
+
+def run_cmd(cmd):
+    proc = subprocess.Popen(
+                cmd,
+                shell=True,
+                stdin=subprocess.PIPE,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE
+            )
+    stdout, stderr = proc.communicate()
+
+    return (
+        stdout.decode("utf-8").strip(),
+        stderr.decode("utf-8").strip(),
+        proc.returncode
+    )
+
+
+def get_tool_version():
+    get_tool_version_cmd = "samtools --version | grep '^samtools'"
+    stdout, stderr, returncode = run_cmd(get_tool_version_cmd)
+    if returncode:
+        sys.exit(f"Error: unable to get version info for samtools.\nStdout: {stdout}\nStderr: {stderr}\n")
+
+    return stdout.strip().split(' ')[-1]
+
+
+def prep_qc_metrics(agg_bamstat, tool_ver):
+    qc_metrics = {
+        'tool': {
+            'name': 'samtools:stats',
+            'version': tool_ver
+        },
+        'metrics': {}
+    }
+
+    collected_sum_fields = {
+        'raw total sequences': 'total_reads',
+        'reads mapped': 'mapped_reads',
+        'reads paired': 'paired_reads',
+        'reads properly paired': 'properly_paired_reads',
+        'pairs on different chromosomes': 'pairs_on_different_chromosomes',
+        'total length': 'total_bases',
+        'bases mapped (cigar)': 'mapped_bases_cigar',
+        'mismatches': 'mismatch_bases',
+        'error rate': 'error_rate',
+        'bases duplicated': 'duplicated_bases',
+        'insert size average': 'average_insert_size',
+        'average length': 'average_length'
+    }
+
+    with open(agg_bamstat, 'r') as f:
+        for row in f:
+            if not row.startswith('SN\t'):
+                continue
+            cols = row.replace(':', '').strip().split('\t')
+            if cols[1] not in collected_sum_fields:
+                continue
+
+            qc_metrics['metrics'].update({
+                collected_sum_fields[cols[1]]: float(cols[2]) if ('.' in cols[2] or 'e' in cols[2]) else int(cols[2])
+            })
+
+    qc_metrics_file = 'qc_metrics.json'
+    with open(qc_metrics_file, "w") as j:
+        j.write(json.dumps(qc_metrics, indent=2))
+
+    return qc_metrics_file
+
+
+def prepare_tarball(aligned_seq, qc_metrics, agg_bamstat, lane_bamstat):
+    tar_content = {
+        'qc_metrics': qc_metrics,
+        'agg_bamstat': agg_bamstat,
+        'lane_bamstat': lane_bamstat
+    }
+
+    with open('tar_content.json', 'w') as t:
+        t.write(json.dumps(tar_content, indent=2))
+
+    files_to_tar = ['tar_content.json', qc_metrics, agg_bamstat] + lane_bamstat
+
+    tarfile_name = f"{os.path.basename(aligned_seq)}.samtools_stats.qc.tgz"
+    with tarfile.open(tarfile_name, "w:gz") as tar:
+        for f in files_to_tar:
+            tar.add(f, arcname=os.path.basename(f))
+
+
+def main(aligned_seq, reference, threads=1):
+    # get samtools version info
+    tool_ver = get_tool_version()
+
+    # run samtools stats
+    stats_args = [
+        '--reference', reference,
+        '-@', str(threads),
+        '-r', reference,
+        '--split', 'RG',
+        '-P', os.path.join(os.getcwd(), os.path.basename(aligned_seq))
+    ]
+
+    cmd = ['samtools', 'stats'] + stats_args + [aligned_seq]
+    stdout, stderr, returncode = run_cmd(" ".join(cmd))
+    if returncode:
+        sys.exit(f"Error: 'samtools stats' failed.\nStdout: {stdout}\nStderr: {stderr}\n")
+
+    agg_bamstat = f"{os.path.basename(aligned_seq)}.bamstat"
+    with open(agg_bamstat, 'w') as f:
+        f.write(stdout)
+
+    # parse samtools stats output and put it in qc_metrics.json
+    qc_metrics_file = prep_qc_metrics(agg_bamstat, tool_ver)
+
+    lane_bamstat = []
+    for f in sorted(glob('*.bamstat')):
+        if f != agg_bamstat:
+            lane_bamstat.append(f)
+
+    # prepare tarball to include output files and qc_metrics.json
+    prepare_tarball(aligned_seq, qc_metrics_file, agg_bamstat, lane_bamstat)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Tool: samtools-stats')
+    parser.add_argument('-s', '--aligned_seq', type=str,
+                        help='Input aligned seq', required=True)
+    parser.add_argument('-r', '--reference', type=str,
+                        help='Reference genome', required=True)
+    parser.add_argument('-t', '--threads', type=int, default=cpu_count(),
+                        help='Number of threads')
+    args = parser.parse_args()
+
+    if not os.path.isfile(args.aligned_seq):
+        sys.exit('Error: specified aligned seq file %s does not exist or is not accessible!' % args.aligned_seq)
+
+    if not os.path.isfile(args.reference):
+        sys.exit('Error: specified reference file %s does not exist or is not accessible!' % args.reference)
+
+    main(args.aligned_seq, args.reference, args.threads)
diff --git a/samtools-stats/nextflow.config b/samtools-stats/nextflow.config
new file mode 100644
index 0000000..f2cd1e3
--- /dev/null
+++ b/samtools-stats/nextflow.config
@@ -0,0 +1,4 @@
+docker {
+    enabled = true
+    runOptions = '-u \$(id -u):\$(id -g)'
+}
diff --git a/samtools-stats/pkg.json b/samtools-stats/pkg.json
new file mode 100644
index 0000000..6056c9d
--- /dev/null
+++ b/samtools-stats/pkg.json
@@ -0,0 +1,39 @@
+{
+    "name": "samtools-stats",
+    "version": "0.1.0",
+    "description": "Samtools stats",
+    "main": "main.nf",
+    "deprecated": false,
+    "keywords": [
+        "bioinformatics",
+        "seq",
+        "qc metrics"
+    ],
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/icgc-argo-qc-wg/argo-qc-tools.git"
+    },
+    "container": {
+        "registries": [
+            {
+                "registry": "ghcr.io",
+                "type": "docker",
+                "org": "icgc-argo-qc-wg",
+                "default": true
+            }
+        ]
+    },
+    "dependencies": [
+        "github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1"
+    ],
+    "devDependencies": [],
+    "contributors": [
+        {
+            "name": "Junjun Zhang",
+            "email": "junjun.ca@gmail.com"
+        }
+    ],
+    "license": "MIT",
+    "bugReport": "https://github.com/icgc-argo-qc-wg/argo-qc-tools/issues",
+    "homepage": "https://github.com/icgc-argo-qc-wg/argo-qc-tools#readme"
+}
\ No newline at end of file
diff --git a/samtools-stats/tests/checker.nf b/samtools-stats/tests/checker.nf
new file mode 100755
index 0000000..2ad4278
--- /dev/null
+++ b/samtools-stats/tests/checker.nf
@@ -0,0 +1,127 @@
+#!/usr/bin/env nextflow
+
+/*
+  Copyright (c) 2021, ICGC ARGO
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+  Authors:
+    Junjun Zhang
+*/
+
+/*
+ This is an auto-generated checker workflow to test the generated main template workflow, it's
+ meant to illustrate how testing works. Please update to suit your own needs.
+*/
+
+/********************************************************************/
+/* this block is auto-generated based on info from pkg.json where   */
+/* changes can be made if needed, do NOT modify this block manually */
+nextflow.enable.dsl = 2
+version = '0.1.0'  // package version
+
+container = [
+    'ghcr.io': 'ghcr.io/icgc-argo-qc-wg/argo-qc-tools.samtools-stats'
+]
+default_container_registry = 'ghcr.io'
+/********************************************************************/
+
+// universal params
+params.container_registry = ""
+params.container_version = ""
+params.container = ""
+
+// tool specific parmas go here, add / change as needed
+params.aligned_seq = ""
+params.ref_genome_gz = ""  // reference genome: *.fa.gz, index file: *.fa.gz.fai
+params.expected_output = ""
+
+include { samtoolsStats } from '../main'
+include { getSecondaryFiles } from './wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/main.nf'
+
+process file_smart_diff {
+  container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}"
+
+  input:
+    path output_file
+    path expected_file
+
+  output:
+    stdout()
+
+  script:
+    """
+    mkdir output expected
+
+    tar xzf ${output_file} -C output
+    tar xzf ${expected_file} -C expected
+
+    cd output
+    for f in *; do
+      if [ ! -f "../expected/\$f" ]
+      then
+        echo "Test FAILED, found unexpected file: \$f in the output tarball" && exit 1
+      fi
+
+      echo diff \$f ../expected/\$f
+      # we ignore diff from the lines with 'The command line' since they contain dynamic file path
+      EFFECTIVE_DIFF=`diff \$f ../expected/\$f | egrep '<|>' | grep -v ' # The command line was:' || true`
+
+      if [ ! -z "\$EFFECTIVE_DIFF" ]
+      then
+        echo -e "Test FAILED, output file \$f mismatch:\n\$EFFECTIVE_DIFF" && exit 1
+      fi
+    done
+
+    echo "All files match, test PASSED" && exit 0
+    """
+}
+
+
+workflow checker {
+  take:
+    aligned_seq
+    ref_genome_gz
+    ref_genome_gz_idx
+    expected_output
+
+  main:
+    samtoolsStats(
+      aligned_seq,
+      ref_genome_gz,
+      ref_genome_gz_idx
+    )
+
+    file_smart_diff(
+      samtoolsStats.out.qc_tar,
+      expected_output
+    )
+}
+
+
+workflow {
+  checker(
+    file(params.aligned_seq),
+    file(params.ref_genome_gz),
+    Channel.fromPath(
+      getSecondaryFiles(params.ref_genome_gz, ['fai']), checkIfExists: true
+    ).collect(),
+    file(params.expected_output)
+  )
+}
diff --git a/samtools-stats/tests/expected/expected.SA610149.0.20200122.wgs.grch38.cram.samtools_stats.qc.tgz b/samtools-stats/tests/expected/expected.SA610149.0.20200122.wgs.grch38.cram.samtools_stats.qc.tgz
new file mode 100644
index 0000000..0595aa2
Binary files /dev/null and b/samtools-stats/tests/expected/expected.SA610149.0.20200122.wgs.grch38.cram.samtools_stats.qc.tgz differ
diff --git a/samtools-stats/tests/input/README.md b/samtools-stats/tests/input/README.md
new file mode 100644
index 0000000..9df14b7
--- /dev/null
+++ b/samtools-stats/tests/input/README.md
@@ -0,0 +1 @@
+This folder contains tiny data files for testing.
diff --git a/samtools-stats/tests/input/SA610149.0.20200122.wgs.grch38.cram b/samtools-stats/tests/input/SA610149.0.20200122.wgs.grch38.cram
new file mode 100644
index 0000000..e3697f6
Binary files /dev/null and b/samtools-stats/tests/input/SA610149.0.20200122.wgs.grch38.cram differ
diff --git a/samtools-stats/tests/input/tiny-grch38-chr11-530001-537000.fa.gz b/samtools-stats/tests/input/tiny-grch38-chr11-530001-537000.fa.gz
new file mode 100644
index 0000000..4669945
Binary files /dev/null and b/samtools-stats/tests/input/tiny-grch38-chr11-530001-537000.fa.gz differ
diff --git a/samtools-stats/tests/input/tiny-grch38-chr11-530001-537000.fa.gz.fai b/samtools-stats/tests/input/tiny-grch38-chr11-530001-537000.fa.gz.fai
new file mode 100644
index 0000000..88de907
--- /dev/null
+++ b/samtools-stats/tests/input/tiny-grch38-chr11-530001-537000.fa.gz.fai
@@ -0,0 +1 @@
+chr11	537000	40	50	51
diff --git a/samtools-stats/tests/nextflow.config b/samtools-stats/tests/nextflow.config
new file mode 100644
index 0000000..4e214a1
--- /dev/null
+++ b/samtools-stats/tests/nextflow.config
@@ -0,0 +1 @@
+includeConfig '../nextflow.config'
diff --git a/samtools-stats/tests/test-job-1.json b/samtools-stats/tests/test-job-1.json
new file mode 100644
index 0000000..1040a28
--- /dev/null
+++ b/samtools-stats/tests/test-job-1.json
@@ -0,0 +1,8 @@
+{
+    "aligned_seq": "input/SA610149.0.20200122.wgs.grch38.cram",
+    "ref_genome_gz": "input/tiny-grch38-chr11-530001-537000.fa.gz",
+    "expected_output": "expected/expected.SA610149.0.20200122.wgs.grch38.cram.samtools_stats.qc.tgz",
+    "publish_dir": "outdir",
+    "cpus": 2,
+    "mem": 1
+}
diff --git a/samtools-stats/tests/wfpr_modules b/samtools-stats/tests/wfpr_modules
new file mode 120000
index 0000000..de8975c
--- /dev/null
+++ b/samtools-stats/tests/wfpr_modules
@@ -0,0 +1 @@
+../wfpr_modules
\ No newline at end of file
diff --git a/samtools-stats/wfpr_modules b/samtools-stats/wfpr_modules
new file mode 120000
index 0000000..de8975c
--- /dev/null
+++ b/samtools-stats/wfpr_modules
@@ -0,0 +1 @@
+../wfpr_modules
\ No newline at end of file
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/.dockerignore b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/.dockerignore
new file mode 100644
index 0000000..71266ec
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/.dockerignore
@@ -0,0 +1,5 @@
+.gitignore
+.nextflow*
+tests
+work
+outdir
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/.gitignore b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/.gitignore
new file mode 100644
index 0000000..a50828c
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/.gitignore
@@ -0,0 +1,69 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+venv*/
+pyvenv*/
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+.coverage.*
+nosetests.xml
+coverage.xml
+htmlcov
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.idea
+*.iml
+*.komodoproject
+
+# Complexity
+output/*.html
+output/*/index.html
+
+# Sphinx
+docs/_build
+
+.DS_Store
+*~
+.*.sw[po]
+.build
+.ve
+.env
+.cache
+.pytest
+.bootstrap
+.appveyor.token
+*.bak
+*.log
+.vscode
+.python-version
+.nextflow*
+work
+outdir
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/Dockerfile b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/Dockerfile
new file mode 100644
index 0000000..ae0e0c8
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/Dockerfile
@@ -0,0 +1,11 @@
+FROM ubuntu:20.04
+
+LABEL org.opencontainers.image.source https://github.com/icgc-argo/data-processing-utility-tools
+
+RUN groupadd -g 1000 ubuntu && \
+    useradd -l -u 1000 -g ubuntu ubuntu && \
+    install -d -m 0755 -o ubuntu -g ubuntu /home/ubuntu
+
+USER ubuntu
+
+CMD ["/bin/bash"]
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/main.nf b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/main.nf
new file mode 100755
index 0000000..e3eb963
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/main.nf
@@ -0,0 +1,55 @@
+#!/usr/bin/env nextflow
+
+/*
+  Copyright (C) 2021,  Ontario Institute for Cancer Research
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU Affero General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU Affero General Public License for more details.
+
+  You should have received a copy of the GNU Affero General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+  Authors:
+    Junjun Zhang
+*/
+
+/********************************************************************/
+/* this block is auto-generated based on info from pkg.json where   */
+/* changes can be made if needed, do NOT modify this block manually */
+nextflow.enable.dsl = 2
+version = '1.0.1'
+/********************************************************************/
+
+
+// this is kind of like CWL's secondary files
+def getSecondaryFiles(main_file, exts){
+  if (!(exts instanceof List)) {
+    exit 1, "[getSecondaryFiles] param: exts must be a list of strings"
+  }
+
+  def secondaryFiles = []
+  for (ext in exts) {
+    if (ext.startsWith("^")) {
+      ext = ext.replace("^", "")
+      parts = main_file.split("\\.").toList()
+      parts.removeLast()
+      secondaryFiles.add((parts + [ext]).join("."))
+    } else {
+      secondaryFiles.add(main_file + '.' + ext)
+    }
+  }
+  return secondaryFiles
+}
+
+
+// get specific secondary files for BWA alignment, ensure none is missing
+def getBwaSecondaryFiles(main_file){
+  return getSecondaryFiles(main_file, ['fai', 'sa', 'bwt', 'ann', 'amb', 'pac', 'alt'])
+}
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/nextflow.config b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/nextflow.config
new file mode 100644
index 0000000..f2cd1e3
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/nextflow.config
@@ -0,0 +1,4 @@
+docker {
+    enabled = true
+    runOptions = '-u \$(id -u):\$(id -g)'
+}
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/pkg.json b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/pkg.json
new file mode 100644
index 0000000..248548a
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/pkg.json
@@ -0,0 +1,38 @@
+{
+    "name": "helper-functions",
+    "version": "1.0.1",
+    "description": "A collection of helper functions",
+    "main": "main.nf",
+    "deprecated": false,
+    "keywords": [
+        "bioinformatics",
+        "utils",
+        "function",
+        "secondary file"
+    ],
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/icgc-argo/data-processing-utility-tools.git"
+    },
+    "container": {
+        "registries": [
+            {
+                "registry": "ghcr.io",
+                "type": "docker",
+                "org": "icgc-argo",
+                "default": true
+            }
+        ]
+    },
+    "dependencies": [],
+    "devDependencies": [],
+    "contributors": [
+        {
+            "name": "Junjun Zhang",
+            "email": "junjun.ca@gmail.com"
+        }
+    ],
+    "license": "GNU Affero General Public License v3",
+    "bugReport": "https://github.com/icgc-argo/data-processing-utility-tools/issues",
+    "homepage": "https://github.com/icgc-argo/data-processing-utility-tools#readme"
+}
\ No newline at end of file
diff --git a/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/wfpr_modules b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/wfpr_modules
new file mode 120000
index 0000000..1cc74ba
--- /dev/null
+++ b/wfpr_modules/github.com/icgc-argo/data-processing-utility-tools/helper-functions@1.0.1/wfpr_modules
@@ -0,0 +1 @@
+../../../../../wfpr_modules
\ No newline at end of file