Add sentieon star

.github/actions/nf-test/action.yml

@@ -54,12 +54,22 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
+     # Set up secrets
+    - name: Set up Nextflow secrets
+      if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
+      shell: bash
+      run: |
+        python -m pip install cryptography
+        nextflow secrets set SENTIEON_AUTH_DATA $(python3 bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
+        SENTIEON_AUTH_MECH: "GitHub Actions - token"
       run: |
         nf-test test \
           --profile=+${{ inputs.profile }} \

bin/license_message.py

@@ -0,0 +1,113 @@
+#!/usr/bin/env python3
+
+#########################################
+# Author: [DonFreed](https://github.com/DonFreed)
+# File: license_message.py
+# Source: https://github.com/DonFreed/docker-actions-test/blob/main/.github/scripts/license_message.py
+# Source+commit: https://github.com/DonFreed/docker-actions-test/blob/aa1051a9f53b3a1e801953748d062cad74dca9a9/.github/scripts/license_message.py
+# Download Date: 2023-07-04, commit: aa1051a
+# This source code is licensed under the BSD 2-Clause license
+#########################################
+
+"""
+Functions for generating and sending license messages
+"""
+
+# Modified from - https://stackoverflow.com/a/59835994
+
+import argparse
+import base64
+import calendar
+import re
+import secrets
+import sys
+
+from cryptography.hazmat.primitives.ciphers.aead import AESGCM
+from datetime import datetime as dt
+
+MESSAGE_TIMEOUT = 60 * 60 * 24  # Messages are valid for 1 day
+NONCE_BYTES = 12
+
+
+class DecryptionTimeout(Exception):
+    # Decrypting a message that is too old
+    pass
+
+
+def generate_key():
+    key = secrets.token_bytes(32)
+    return key
+
+
+def handle_generate_key(args):
+    key = generate_key()
+    key_b64 = base64.b64encode(key)
+    print(key_b64.decode("utf-8"), file=args.outfile)
+
+
+def encrypt_message(key, message):
+    nonce = secrets.token_bytes(NONCE_BYTES)
+    timestamp = calendar.timegm(dt.now().utctimetuple())
+    data = timestamp.to_bytes(10, byteorder="big") + b"__" + message
+    ciphertext = nonce + AESGCM(key).encrypt(nonce, data, b"")
+    return ciphertext
+
+
+def handle_encrypt_message(args):
+    key = base64.b64decode(args.key.encode("utf-8"))
+    message = args.message.encode("utf-8")
+    ciphertext = encrypt_message(key, message)
+    ciphertext_b64 = base64.b64encode(ciphertext)
+    print(ciphertext_b64.decode("utf-8"), file=args.outfile)
+
+
+def decrypt_message(key, ciphertext, timeout=MESSAGE_TIMEOUT):
+    nonce, ciphertext = ciphertext[:NONCE_BYTES], ciphertext[NONCE_BYTES:]
+    message = AESGCM(key).decrypt(nonce, ciphertext, b"")
+
+    msg_timestamp, message = re.split(b"__", message, maxsplit=1)
+    msg_timestamp = int.from_bytes(msg_timestamp, byteorder="big")
+    timestamp = calendar.timegm(dt.now().utctimetuple())
+    if (timestamp - msg_timestamp) > timeout:
+        raise DecryptionTimeout("The message has an expired timeout")
+    return message.decode("utf-8")
+
+
+def handle_decrypt_message(args):
+    key = base64.b64decode(args.key.encode("utf-8"))
+    ciphertext = base64.b64decode(args.message.encode("utf-8"))
+    message = decrypt_message(key, ciphertext, timeout=args.timeout)
+    print(str(message), file=args.outfile)
+
+
+def parse_args(argv=None):
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--outfile", default=sys.stdout, type=argparse.FileType("w"), help="The output file")
+
+    subparsers = parser.add_subparsers(help="Available sub-commands")
+
+    gen_parser = subparsers.add_parser("generate_key", help="Generate a random key string")
+    gen_parser.set_defaults(func=handle_generate_key)
+
+    encrypt_parser = subparsers.add_parser("encrypt", help="Encrypt a message")
+    encrypt_parser.add_argument("--key", required=True, help="The encryption key")
+    encrypt_parser.add_argument("--message", required=True, help="Message to encrypt")
+    encrypt_parser.set_defaults(func=handle_encrypt_message)
+
+    decrypt_parser = subparsers.add_parser("decrypt", help="Decyrpt a message")
+    decrypt_parser.add_argument("--key", required=True, help="The encryption key")
+    decrypt_parser.add_argument("--message", required=True, help="Message to decrypt")
+    decrypt_parser.add_argument(
+        "--timeout",
+        default=MESSAGE_TIMEOUT,
+        type=int,
+        help="A message timeout. Decryption will fail for older messages",
+    )
+    decrypt_parser.set_defaults(func=handle_decrypt_message)
+
+    return parser.parse_args(argv)
+
+
+if __name__ == "__main__":
+    args = parse_args()
+    args.func(args)

modules.json

@@ -217,6 +217,11 @@
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["bam_stats_samtools"]
                     },
+                    "sentieon/staralign": {
+                        "branch": "master",
+                        "git_sha": "73d3ab1ac411843ae643b5bc310a4aec9ae7ab3a",
+                        "installed_by": ["modules"]
+                    },
                     "sortmerna": {
                         "branch": "master",
                         "git_sha": "d4a425ce59fc803a11e520f16680ede9af09761f",