Merge branch 'cw-2098' into 'dev'

aws demo

See merge request epi2melabs/workflows/wf-mpx!20

.gitignore

@@ -3,3 +3,5 @@ nextflow
 template-workflow
 .*.swp
 .*.swo
+*.pyc
+*.pyo

.pre-commit-config.yaml

@@ -18,9 +18,10 @@ repos:
         additional_dependencies:
           - epi2melabs
   - repo: https://github.com/pycqa/flake8
-    rev: 3.7.9
+    rev: 5.0.4
     hooks:
       - id: flake8
+        pass_filenames: false
         additional_dependencies:
           - flake8-rst-docstrings
           - flake8-docstrings
@@ -31,4 +32,9 @@ repos:
           - flake8-builtins
           - flake8-absolute-import
           - flake8-print
-        entry: flake8 bin --import-order-style google --statistics
+        args: [
+            "bin",
+            "--import-order-style=google",
+            "--statistics",
+            "--max-line-length=88",
+        ]

CHANGELOG.md

@@ -1,9 +1,15 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.0.7]
+### Changed
+- Updated whole workflow to bring up-to-date with recent template changes
+### Added
+- Configuration for running demo data in AWS
+
 ## [v0.0.6]
 ### Changed
 - Updated description in manifest

LICENSE

@@ -1,12 +1,5 @@
-This Source Code Form is subject to the terms of the Mozilla Public
-License, v. 2.0. If a copy of the MPL was not distributed with this
-file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-(c) 2021- Oxford Nanopore Technologies Ltd.
-
-
-Mozilla Public License Version 2.0
-==================================
+Oxford Nanopore Technologies PLC. Public License Version 1.0
+=============================================================
 
 1. Definitions
 --------------
@@ -17,7 +10,7 @@ Mozilla Public License Version 2.0
 
 1.2. "Contributor Version"
     means the combination of the Contributions of others (if any) used
-    by a Contributor and that particular Contributor's Contribution.
+    by a Contributor and that particular Contributor’s Contribution.
 
 1.3. "Contribution"
     means Covered Software of a particular Contributor.
@@ -28,59 +21,46 @@ Mozilla Public License Version 2.0
     Form, and Modifications of such Source Code Form, in each case
     including portions thereof.
 
-1.5. "Incompatible With Secondary Licenses"
-    means
-
-    (a) that the initial Contributor has attached the notice described
-        in Exhibit B to the Covered Software; or
-
-    (b) that the Covered Software was made available under the terms of
-        version 1.1 or earlier of the License, but not also under the
-        terms of a Secondary License.
-
-1.6. "Executable Form"
+1.5. "Executable Form"
     means any form of the work other than Source Code Form.
 
-1.7. "Larger Work"
+1.6. "Larger Work"
     means a work that combines Covered Software with other material, in
     a separate file or files, that is not Covered Software.
 
-1.8. "License"
+1.7. "License"
     means this document.
 
-1.9. "Licensable"
+1.8. "Licensable"
     means having the right to grant, to the maximum extent possible,
     whether at the time of the initial grant or subsequently, any and
     all of the rights conveyed by this License.
 
-1.10. "Modifications"
+1.9. "Modifications"
     means any of the following:
 
-    (a) any file in Source Code Form that results from an addition to,
-        deletion from, or modification of the contents of Covered
-        Software; or
-
-    (b) any new file in Source Code Form that contains any Covered
-        Software.
+    (a)	  any file in Source Code Form that results from an addition to,
+          deletion from, or modification of the contents of Covered
+          Software; or
+    (b)   any new file in Source Code Form that contains any Covered
+          Software.
 
-1.11. "Patent Claims" of a Contributor
-    means any patent claim(s), including without limitation, method,
-    process, and apparatus claims, in any patent Licensable by such
-    Contributor that would be infringed, but for the grant of the
-    License, by the making, using, selling, offering for sale, having
-    made, import, or transfer of either its Contributions or its
-    Contributor Version.
+1.10. "Research Purposes"
+    means use for internal research and not intended for or directed
+    towards commercial advantages or monetary compensation; provided,
+    however, that monetary compensation does not include sponsored
+    research of research funded by grants.
 
-1.12. "Secondary License"
+1.11  "Secondary License"
     means either the GNU General Public License, Version 2.0, the GNU
     Lesser General Public License, Version 2.1, the GNU Affero General
     Public License, Version 3.0, or any later versions of those
     licenses.
 
-1.13. "Source Code Form"
+1.12. "Source Code Form"
     means the form of the work preferred for making modifications.
 
-1.14. "You" (or "Your")
+1.13. "You" (or "Your")
     means an individual or a legal entity exercising rights under this
     License. For legal entities, "You" includes any entity that
     controls, is controlled by, or is under common control with You. For
@@ -96,53 +76,47 @@ Mozilla Public License Version 2.0
 2.1. Grants
 
 Each Contributor hereby grants You a world-wide, royalty-free,
-non-exclusive license:
-
-(a) under intellectual property rights (other than patent or trademark)
-    Licensable by such Contributor to use, reproduce, make available,
-    modify, display, perform, distribute, and otherwise exploit its
-    Contributions, either on an unmodified basis, with Modifications, or
-    as part of a Larger Work; and
-
-(b) under Patent Claims of such Contributor to make, use, sell, offer
-    for sale, have made, import, and otherwise transfer either its
-    Contributions or its Contributor Version.
+non-exclusive license under Contributor copyrights Licensable by such
+Contributor to use, reproduce, make available, modify, display,
+perform, distribute, and otherwise exploit solely for Research Purposes
+its Contributions, either on an unmodified basis, with Modifications,
+or as part of a Larger Work.
 
 2.2. Effective Date
 
 The licenses granted in Section 2.1 with respect to any Contribution
-become effective for each Contribution on the date the Contributor first
-distributes such Contribution.
+become effective for each Contribution on the date the Contributor
+first distributes such Contribution.
 
 2.3. Limitations on Grant Scope
 
 The licenses granted in this Section 2 are the only rights granted under
 this License. No additional rights or licenses will be implied from the
-distribution or licensing of Covered Software under this License.
-Notwithstanding Section 2.1(b) above, no patent license is granted by a
-Contributor:
+distribution or licensing of Covered Software under this License. The
+License is incompatible with Secondary Licenses.  Notwithstanding
+Section 2.1 above, no copyright license is granted:
 
 (a) for any code that a Contributor has removed from Covered Software;
     or
 
-(b) for infringements caused by: (i) Your and any other third party's
-    modifications of Covered Software, or (ii) the combination of its
-    Contributions with other software (except as part of its Contributor
-    Version); or
+(b) use of the Contributions or its Contributor Version other than for
+Research Purposes only; or
 
-(c) under Patent Claims infringed by Covered Software in the absence of
-    its Contributions.
+(c) for infringements caused by: (i) Your and any other third party’s
+modifications of Covered Software, or (ii) the combination of its
+Contributions with other software (except as part of its Contributor
+Version).
 
-This License does not grant any rights in the trademarks, service marks,
-or logos of any Contributor (except as may be necessary to comply with
-the notice requirements in Section 3.4).
+This License does not grant any rights in the patents, trademarks,
+service marks, or logos of any Contributor (except as may be necessary
+to comply with the notice requirements in Section 3.4).
 
 2.4. Subsequent Licenses
 
 No Contributor makes additional grants as a result of Your choice to
 distribute the Covered Software under a subsequent version of this
-License (see Section 10.2) or under the terms of a Secondary License (if
-permitted under the terms of Section 3.3).
+License (see Section 10.2) or under the terms of a Secondary License
+(if permitted under the terms of Section 3.3).
 
 2.5. Representation
 
@@ -171,8 +145,7 @@ Modifications that You create or to which You contribute, must be under
 the terms of this License. You must inform recipients that the Source
 Code Form of the Covered Software is governed by the terms of this
 License, and how they can obtain a copy of this License. You may not
-attempt to alter or restrict the recipients' rights in the Source Code
-Form.
+attempt to alter or restrict the recipients’ rights in the Source Code Form.
 
 3.2. Distribution of Executable Form
 
@@ -185,22 +158,14 @@ If You distribute Covered Software in Executable Form then:
     than the cost of distribution to the recipient; and
 
 (b) You may distribute such Executable Form under the terms of this
-    License, or sublicense it under different terms, provided that the
-    license for the Executable Form does not attempt to limit or alter
-    the recipients' rights in the Source Code Form under this License.
+    License.
 
 3.3. Distribution of a Larger Work
 
 You may create and distribute a Larger Work under terms of Your choice,
 provided that You also comply with the requirements of this License for
-the Covered Software. If the Larger Work is a combination of Covered
-Software with a work governed by one or more Secondary Licenses, and the
-Covered Software is not Incompatible With Secondary Licenses, this
-License permits You to additionally distribute such Covered Software
-under the terms of such Secondary License(s), so that the recipient of
-the Larger Work may, at their option, further distribute the Covered
-Software under the terms of either this License or such Secondary
-License(s).
+the Covered Software. The Larger Work may not be a combination of Covered
+Software with a work governed by one or more Secondary Licenses.
 
 3.4. Notices
 
@@ -212,16 +177,15 @@ the extent required to remedy known factual inaccuracies.
 
 3.5. Application of Additional Terms
 
-You may choose to offer, and to charge a fee for, warranty, support,
-indemnity or liability obligations to one or more recipients of Covered
-Software. However, You may do so only on Your own behalf, and not on
-behalf of any Contributor. You must make it absolutely clear that any
-such warranty, support, indemnity, or liability obligation is offered by
-You alone, and You hereby agree to indemnify every Contributor for any
-liability incurred by such Contributor as a result of warranty, support,
-indemnity or liability terms You offer. You may include additional
-disclaimers of warranty and limitations of liability specific to any
-jurisdiction.
+You may not choose to offer, or charge a fee for use of the Covered
+Software or a fee for, warranty, support, indemnity or liability
+obligations to one or more recipients of Covered Software.  You must
+make it absolutely clear that any such warranty, support, indemnity, or
+liability obligation is offered by You alone, and You hereby agree to
+indemnify every Contributor for any liability incurred by such
+Contributor as a result of warranty, support, indemnity or liability
+terms You offer. You may include additional disclaimers of warranty and
+limitations of liability specific to any jurisdiction.
 
 4. Inability to Comply Due to Statute or Regulation
 ---------------------------------------------------
@@ -240,23 +204,12 @@ recipient of ordinary skill to be able to understand it.
 --------------
 
 5.1. The rights granted under this License will terminate automatically
-if You fail to comply with any of its terms. However, if You become
-compliant, then the rights granted under this License from a particular
-Contributor are reinstated (a) provisionally, unless and until such
-Contributor explicitly and finally terminates Your grants, and (b) on an
-ongoing basis, if such Contributor fails to notify You of the
-non-compliance by some reasonable means prior to 60 days after You have
-come back into compliance. Moreover, Your grants from a particular
-Contributor are reinstated on an ongoing basis if such Contributor
-notifies You of the non-compliance by some reasonable means, this is the
-first time You have received notice of non-compliance with this License
-from such Contributor, and You become compliant prior to 30 days after
-Your receipt of the notice.
-
-5.2. If You initiate litigation against any entity by asserting a patent
+if You fail to comply with any of its terms.
+
+5.2. If You initiate litigation against any entity by asserting an
 infringement claim (excluding declaratory judgment actions,
 counter-claims, and cross-claims) alleging that a Contributor Version
-directly or indirectly infringes any patent, then the rights granted to
+directly or indirectly infringes, then the rights granted to
 You by any and all Contributors for the Covered Software under Section
 2.1 of this License shall terminate.
 
@@ -299,8 +252,10 @@ prior to termination shall survive termination.
 *  and all other commercial damages or losses, even if such party      *
 *  shall have been informed of the possibility of such damages. This   *
 *  limitation of liability shall not apply to liability for death or   *
-*  personal injury resulting from such party's negligence to the       *
-*  extent applicable law prohibits such limitation. Some               *
+*  personal injury resulting from such party’s negligence to the       *
+*  extent applicable law prohibits such limitation, but in such event, *
+*  and to the greatest extent permissible, damages will be limited to  *
+*  direct damages not to exceed one hundred dollars. Some              *
 *  jurisdictions do not allow the exclusion or limitation of           *
 *  incidental or consequential damages, so this exclusion and          *
 *  limitation may not apply to You.                                    *
@@ -314,7 +269,7 @@ Any litigation relating to this License may be brought only in the
 courts of a jurisdiction where the defendant maintains its principal
 place of business and such litigation shall be governed by laws of that
 jurisdiction, without reference to its conflict-of-law provisions.
-Nothing in this Section shall prevent a party's ability to bring
+Nothing in this Section shall prevent a party’s ability to bring
 cross-claims or counter-claims.
 
 9. Miscellaneous
@@ -332,10 +287,10 @@ shall not be used to construe this License against a Contributor.
 
 10.1. New Versions
 
-Mozilla Foundation is the license steward. Except as provided in Section
-10.3, no one other than the license steward has the right to modify or
-publish new versions of this License. Each version will be given a
-distinguishing version number.
+Oxford Nanopore Technologies PLC. is the license steward. Except as
+provided in Section 10.3, no one other than the license steward has the
+right to modify or publish new versions of this License. Each version
+will be given a distinguishing version number.
 
 10.2. Effect of New Versions
 
@@ -352,29 +307,16 @@ modified version of this License if you rename the license and remove
 any references to the name of the license steward (except to note that
 such modified license differs from this License).
 
-10.4. Distributing Source Code Form that is Incompatible With Secondary
-Licenses
-
-If You choose to distribute Source Code Form that is Incompatible With
-Secondary Licenses under the terms of this version of the License, the
-notice described in Exhibit B of this License must be attached.
-
 Exhibit A - Source Code Form License Notice
 -------------------------------------------
 
-  This Source Code Form is subject to the terms of the Mozilla Public
-  License, v. 2.0. If a copy of the MPL was not distributed with this
-  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+  This Source Code Form is subject to the terms of the Oxford Nanopore
+  Technologies PLC. Public License, v. 1.0. Full licence can be found
+  obtained from [email protected]
 
 If it is not possible or desirable to put the notice in a particular
 file, then You may include the notice in a location (such as a LICENSE
 file in a relevant directory) where a recipient would be likely to look
 for such a notice.
 
 You may add additional accurate notices of copyright ownership.
-
-Exhibit B - "Incompatible With Secondary Licenses" Notice
----------------------------------------------------------
-
-  This Source Code Form is "Incompatible With Secondary Licenses", as
-  defined by the Mozilla Public License, v. 2.0.