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Sync all - improvements #709

Closed
ewels opened this issue Jul 30, 2020 · 2 comments
Closed

Sync all - improvements #709

ewels opened this issue Jul 30, 2020 · 2 comments

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@ewels
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ewels commented Jul 30, 2020

We need to go through the the v1.10.1 sync log and see what to fix / improve.

Final summary:

 INFO      Finished. Successfully synchronised 31 pipelines           sync.py:403
 ERROR     Errors whilst synchronising 12 pipelines:                  sync.py:407
            - ampliseq
            - artic
            - bcellmagic
            - clinvap
            - deepvariant
            - exoseq
            - hlatyping
            - kmermaid
            - mag
            - mhcquant
            - nascent
            - vipr

Learning from my mistakes and posting here as well in case the above action logs expire and are deleted:

logs_2307.zip

6_Run synchronisation.txt 
2020-07-30T20:03:58.5458628Z ##[group]Run git config --global user.email "core@nf-co.re"
2020-07-30T20:03:58.5458896Z �[36;1mgit config --global user.email "core@nf-co.re"�[0m
2020-07-30T20:03:58.5459002Z �[36;1mgit config --global user.name "nf-core-bot"�[0m
2020-07-30T20:03:58.5459128Z �[36;1mnf-core --log-file sync_log.txt sync --all --username nf-core-bot --auth-token $AUTH_TOKEN�[0m
2020-07-30T20:03:58.5492295Z shell: /bin/bash -e {0}
2020-07-30T20:03:58.5492413Z env:
2020-07-30T20:03:58.5492528Z   pythonLocation: /opt/hostedtoolcache/Python/3.8.5/x64
2020-07-30T20:03:58.5493079Z   AUTH_TOKEN: ***
2020-07-30T20:03:58.5493200Z ##[endgroup]
2020-07-30T20:04:00.1440787Z
2020-07-30T20:04:00.1442238Z                                           ,--./,-.
2020-07-30T20:04:00.1449792Z           ___     __   __   __   ___     /,-._.--~\
2020-07-30T20:04:00.1458629Z     |\ | |__  __ /  ` /  \ |__) |__         }  {
2020-07-30T20:04:00.1465913Z     | \| |       \__, \__/ |  \ |___     \`-._,-`-,
2020-07-30T20:04:00.1473392Z                                           `._,._,'
2020-07-30T20:04:00.1473824Z
2020-07-30T20:04:00.1479337Z     nf-core/tools version 1.10.1
2020-07-30T20:04:00.9227146Z
2020-07-30T20:04:00.9227443Z
2020-07-30T20:04:00.9227506Z
2020-07-30T20:04:01.7950557Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:04:01.7966058Z INFO      Syncing nf-core/ampliseq                                   sync.py:358
2020-07-30T20:04:02.7788177Z INFO      Pipeline directory: /tmp/tmphb7smj55/ampliseq               sync.py:87
2020-07-30T20:04:02.7788884Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:04:02.7789283Z             Will attempt to automatically create a pull request on
2020-07-30T20:04:02.7789639Z           github.com
2020-07-30T20:04:12.4055652Z ERROR     Sync failed for nf-core/ampliseq:                          sync.py:385
2020-07-30T20:04:12.4056003Z           GitHub API returned code 422:
2020-07-30T20:04:12.4056186Z           {
2020-07-30T20:04:12.4056344Z               "message": "Validation Failed",
2020-07-30T20:04:12.4056496Z               "errors": [
2020-07-30T20:04:12.4056648Z                   {
2020-07-30T20:04:12.4056983Z                       "resource": "PullRequest",
2020-07-30T20:04:12.4057137Z                       "code": "custom",
2020-07-30T20:04:12.4057514Z                       "message": "A pull request already exists for
2020-07-30T20:04:12.4058126Z           nf-core:TEMPLATE."
2020-07-30T20:04:12.4058288Z                   }
2020-07-30T20:04:12.4058443Z               ],
2020-07-30T20:04:12.4058643Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:04:12.4059003Z           pulls/#create-a-pull-request"
2020-07-30T20:04:12.4059156Z           }
2020-07-30T20:04:12.4104287Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:04:12.4118497Z INFO      Syncing nf-core/artic                                      sync.py:358
2020-07-30T20:04:12.9738751Z INFO      Pipeline directory: /tmp/tmphb7smj55/artic                  sync.py:87
2020-07-30T20:04:12.9739678Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:04:12.9740138Z             Will attempt to automatically create a pull request on
2020-07-30T20:04:12.9740580Z           github.com
2020-07-30T20:04:20.8859890Z ERROR     Sync failed for nf-core/artic:                             sync.py:385
2020-07-30T20:04:20.8860709Z           GitHub API returned code 422:
2020-07-30T20:04:20.8861141Z           {
2020-07-30T20:04:20.8862076Z               "message": "Validation Failed",
2020-07-30T20:04:20.8862579Z               "errors": [
2020-07-30T20:04:20.8862902Z                   {
2020-07-30T20:04:20.8863226Z                       "resource": "PullRequest",
2020-07-30T20:04:20.8863594Z                       "code": "custom",
2020-07-30T20:04:20.8863922Z                       "message": "A pull request already exists for
2020-07-30T20:04:20.8864508Z           nf-core:TEMPLATE."
2020-07-30T20:04:20.8864902Z                   }
2020-07-30T20:04:20.8865413Z               ],
2020-07-30T20:04:20.8865788Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:04:20.8866693Z           pulls/#create-a-pull-request"
2020-07-30T20:04:20.8867127Z           }
2020-07-30T20:04:20.8899709Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:04:20.8912781Z INFO      Syncing nf-core/atacseq                                    sync.py:358
2020-07-30T20:04:21.7840815Z INFO      Pipeline directory: /tmp/tmphb7smj55/atacseq                sync.py:87
2020-07-30T20:04:21.7841487Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:04:21.7841930Z             Will attempt to automatically create a pull request on
2020-07-30T20:04:21.7842093Z           github.com
2020-07-30T20:04:31.4185416Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:04:31.4187154Z           https://github.com/nf-core/atacseq/pull/120
2020-07-30T20:04:31.4415959Z INFO      Sync successful for nf-core/atacseq:                       sync.py:391
2020-07-30T20:04:31.4416749Z           https://github.com/nf-core/atacseq/pull/120
2020-07-30T20:04:31.4480472Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:04:31.4498563Z INFO      Syncing nf-core/bacass                                     sync.py:358
2020-07-30T20:04:32.0871455Z INFO      Pipeline directory: /tmp/tmphb7smj55/bacass                 sync.py:87
2020-07-30T20:04:32.0871761Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:04:32.0871903Z             Will attempt to automatically create a pull request on
2020-07-30T20:04:32.0872037Z           github.com
2020-07-30T20:04:41.2082256Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:04:41.2083264Z           https://github.com/nf-core/bacass/pull/29
2020-07-30T20:04:41.2280034Z INFO      Sync successful for nf-core/bacass:                        sync.py:391
2020-07-30T20:04:41.2280800Z           https://github.com/nf-core/bacass/pull/29
2020-07-30T20:04:41.2349786Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:04:41.2366183Z INFO      Syncing nf-core/bactmap                                    sync.py:358
2020-07-30T20:04:41.7300440Z INFO      Pipeline directory: /tmp/tmphb7smj55/bactmap                sync.py:87
2020-07-30T20:04:41.7301630Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:04:41.7302025Z             Will attempt to automatically create a pull request on
2020-07-30T20:04:41.7302174Z           github.com
2020-07-30T20:04:51.1654243Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:04:51.1655694Z           https://github.com/nf-core/bactmap/pull/4
2020-07-30T20:04:51.1766528Z INFO      Sync successful for nf-core/bactmap:                       sync.py:391
2020-07-30T20:04:51.1767288Z           https://github.com/nf-core/bactmap/pull/4
2020-07-30T20:04:51.1827918Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:04:51.1845553Z INFO      Syncing nf-core/bcellmagic                                 sync.py:358
2020-07-30T20:04:51.8316780Z INFO      Pipeline directory: /tmp/tmphb7smj55/bcellmagic             sync.py:87
2020-07-30T20:04:51.8317467Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:04:51.8317825Z             Will attempt to automatically create a pull request on
2020-07-30T20:04:51.8318150Z           github.com
2020-07-30T20:05:00.9705001Z ERROR     Sync failed for nf-core/bcellmagic:                        sync.py:385
2020-07-30T20:05:00.9705799Z           GitHub API returned code 422:
2020-07-30T20:05:00.9706250Z           {
2020-07-30T20:05:00.9706629Z               "message": "Validation Failed",
2020-07-30T20:05:00.9707158Z               "errors": [
2020-07-30T20:05:00.9707503Z                   {
2020-07-30T20:05:00.9708027Z                       "resource": "PullRequest",
2020-07-30T20:05:00.9708366Z                       "code": "custom",
2020-07-30T20:05:00.9708702Z                       "message": "A pull request already exists for
2020-07-30T20:05:00.9709298Z           nf-core:TEMPLATE."
2020-07-30T20:05:00.9709890Z                   }
2020-07-30T20:05:00.9710274Z               ],
2020-07-30T20:05:00.9710670Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:05:00.9711290Z           pulls/#create-a-pull-request"
2020-07-30T20:05:00.9711858Z           }
2020-07-30T20:05:00.9763150Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:05:00.9776692Z INFO      Syncing nf-core/cageseq                                    sync.py:358
2020-07-30T20:05:01.7558820Z INFO      Pipeline directory: /tmp/tmphb7smj55/cageseq                sync.py:87
2020-07-30T20:05:01.7559449Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:05:01.7559991Z             Will attempt to automatically create a pull request on
2020-07-30T20:05:01.7560493Z           github.com
2020-07-30T20:05:11.0053133Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:05:11.0054513Z           https://github.com/nf-core/cageseq/pull/12
2020-07-30T20:05:11.0169835Z INFO      Sync successful for nf-core/cageseq:                       sync.py:391
2020-07-30T20:05:11.0170793Z           https://github.com/nf-core/cageseq/pull/12
2020-07-30T20:05:11.0232888Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:05:11.0248995Z INFO      Syncing nf-core/chipseq                                    sync.py:358
2020-07-30T20:05:12.1274330Z INFO      Pipeline directory: /tmp/tmphb7smj55/chipseq                sync.py:87
2020-07-30T20:05:12.1276444Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:05:12.1276623Z             Will attempt to automatically create a pull request on
2020-07-30T20:05:12.1277354Z           github.com
2020-07-30T20:05:21.3689583Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:05:21.3690867Z           https://github.com/nf-core/chipseq/pull/176
2020-07-30T20:05:21.3905220Z INFO      Sync successful for nf-core/chipseq:                       sync.py:391
2020-07-30T20:05:21.3906012Z           https://github.com/nf-core/chipseq/pull/176
2020-07-30T20:05:21.3971225Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:05:21.3985499Z INFO      Syncing nf-core/clinvap                                    sync.py:358
2020-07-30T20:05:22.7367919Z INFO      Pipeline directory: /tmp/tmphb7smj55/clinvap                sync.py:87
2020-07-30T20:05:22.7368534Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:05:22.7368773Z             Will attempt to automatically create a pull request on
2020-07-30T20:05:22.7368911Z           github.com
2020-07-30T20:05:25.2065427Z ERROR     Sync failed for nf-core/clinvap:                           sync.py:385
2020-07-30T20:05:25.2066496Z           Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'
2020-07-30T20:05:25.2205272Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:05:25.2212447Z INFO      Syncing nf-core/coproid                                    sync.py:358
2020-07-30T20:05:30.2228449Z INFO      Pipeline directory: /tmp/tmphb7smj55/coproid                sync.py:87
2020-07-30T20:05:30.2229102Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:05:30.2229450Z             Will attempt to automatically create a pull request on
2020-07-30T20:05:30.2229757Z           github.com
2020-07-30T20:05:39.8789612Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:05:39.8790826Z           https://github.com/nf-core/coproid/pull/30
2020-07-30T20:05:39.9352054Z INFO      Sync successful for nf-core/coproid:                       sync.py:391
2020-07-30T20:05:39.9353157Z           https://github.com/nf-core/coproid/pull/30
2020-07-30T20:05:39.9440231Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:05:39.9453543Z INFO      Syncing nf-core/crisprvar                                  sync.py:358
2020-07-30T20:05:43.1049120Z INFO      Pipeline directory: /tmp/tmphb7smj55/crisprvar              sync.py:87
2020-07-30T20:05:43.1049757Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:05:43.1050140Z             Will attempt to automatically create a pull request on
2020-07-30T20:05:43.1050800Z           github.com
2020-07-30T20:05:52.2871099Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:05:52.2872617Z           https://github.com/nf-core/crisprvar/pull/3
2020-07-30T20:05:52.3185292Z INFO      Sync successful for nf-core/crisprvar:                     sync.py:391
2020-07-30T20:05:52.3186303Z           https://github.com/nf-core/crisprvar/pull/3
2020-07-30T20:05:52.3280320Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:05:52.3292743Z INFO      Syncing nf-core/ddamsproteomics                            sync.py:358
2020-07-30T20:05:53.9401081Z INFO      Pipeline directory: /tmp/tmphb7smj55/ddamsproteomics        sync.py:87
2020-07-30T20:05:53.9401779Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:05:53.9402156Z             Will attempt to automatically create a pull request on
2020-07-30T20:05:53.9402507Z           github.com
2020-07-30T20:06:02.3649296Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:06:02.3650775Z           https://github.com/nf-core/ddamsproteomics/pull/14
2020-07-30T20:06:02.3755014Z INFO      Sync successful for nf-core/ddamsproteomics:               sync.py:391
2020-07-30T20:06:02.3755773Z           https://github.com/nf-core/ddamsproteomics/pull/14
2020-07-30T20:06:02.3809906Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:06:02.3821991Z INFO      Syncing nf-core/deepvariant                                sync.py:358
2020-07-30T20:06:03.4750277Z INFO      Pipeline directory: /tmp/tmphb7smj55/deepvariant            sync.py:87
2020-07-30T20:06:03.4750952Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:06:03.4751488Z             Will attempt to automatically create a pull request on
2020-07-30T20:06:03.4751978Z           github.com
2020-07-30T20:06:10.7559212Z ERROR     Sync failed for nf-core/deepvariant:                       sync.py:385
2020-07-30T20:06:10.7560092Z           GitHub API returned code 404:
2020-07-30T20:06:10.7560484Z           {
2020-07-30T20:06:10.7560829Z               "message": "Not Found",
2020-07-30T20:06:10.7561631Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:06:10.7563285Z           pulls/#create-a-pull-request"
2020-07-30T20:06:10.7563837Z           }
2020-07-30T20:06:10.7627173Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:06:10.7640913Z INFO      Syncing nf-core/demultiplex                                sync.py:358
2020-07-30T20:06:11.3189459Z INFO      Pipeline directory: /tmp/tmphb7smj55/demultiplex            sync.py:87
2020-07-30T20:06:11.3190141Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:06:11.3190496Z             Will attempt to automatically create a pull request on
2020-07-30T20:06:11.3190819Z           github.com
2020-07-30T20:06:20.9034401Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:06:20.9035743Z           https://github.com/nf-core/demultiplex/pull/12
2020-07-30T20:06:20.9155393Z INFO      Sync successful for nf-core/demultiplex:                   sync.py:391
2020-07-30T20:06:20.9156499Z           https://github.com/nf-core/demultiplex/pull/12
2020-07-30T20:06:20.9220169Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:06:20.9235044Z INFO      Syncing nf-core/denovohybrid                               sync.py:358
2020-07-30T20:06:21.4407233Z INFO      Pipeline directory: /tmp/tmphb7smj55/denovohybrid           sync.py:87
2020-07-30T20:06:21.4407935Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:06:21.4408302Z             Will attempt to automatically create a pull request on
2020-07-30T20:06:21.4408661Z           github.com
2020-07-30T20:06:30.4874520Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:06:30.4875763Z           https://github.com/nf-core/denovohybrid/pull/7
2020-07-30T20:06:30.4976110Z INFO      Sync successful for nf-core/denovohybrid:                  sync.py:391
2020-07-30T20:06:30.4977339Z           https://github.com/nf-core/denovohybrid/pull/7
2020-07-30T20:06:30.5037580Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:06:30.5054207Z INFO      Syncing nf-core/diaproteomics                              sync.py:358
2020-07-30T20:06:31.0680717Z INFO      Pipeline directory: /tmp/tmphb7smj55/diaproteomics          sync.py:87
2020-07-30T20:06:31.0681645Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:06:31.0682155Z             Will attempt to automatically create a pull request on
2020-07-30T20:06:31.0682473Z           github.com
2020-07-30T20:06:40.4504340Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:06:40.4507126Z           https://github.com/nf-core/diaproteomics/pull/28
2020-07-30T20:06:40.4622903Z INFO      Sync successful for nf-core/diaproteomics:                 sync.py:391
2020-07-30T20:06:40.4623666Z           https://github.com/nf-core/diaproteomics/pull/28
2020-07-30T20:06:40.4693618Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:06:40.4706893Z INFO      Syncing nf-core/eager                                      sync.py:358
2020-07-30T20:06:42.8636366Z INFO      Pipeline directory: /tmp/tmphb7smj55/eager                  sync.py:87
2020-07-30T20:06:42.8637269Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:06:42.8637659Z             Will attempt to automatically create a pull request on
2020-07-30T20:06:42.8638196Z           github.com
2020-07-30T20:06:52.5335479Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:06:52.5336849Z           https://github.com/nf-core/eager/pull/533
2020-07-30T20:06:52.6025419Z INFO      Sync successful for nf-core/eager:                         sync.py:391
2020-07-30T20:06:52.6026616Z           https://github.com/nf-core/eager/pull/533
2020-07-30T20:06:52.6119445Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:06:52.6132936Z INFO      Syncing nf-core/epitopeprediction                          sync.py:358
2020-07-30T20:06:53.2517343Z INFO      Pipeline directory: /tmp/tmphb7smj55/epitopeprediction      sync.py:87
2020-07-30T20:06:53.2518048Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:06:53.2518412Z             Will attempt to automatically create a pull request on
2020-07-30T20:06:53.2518759Z           github.com
2020-07-30T20:07:02.3911089Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:07:02.3912790Z           https://github.com/nf-core/epitopeprediction/pull/46
2020-07-30T20:07:02.4021139Z INFO      Sync successful for nf-core/epitopeprediction:             sync.py:391
2020-07-30T20:07:02.4021976Z           https://github.com/nf-core/epitopeprediction/pull/46
2020-07-30T20:07:02.4081518Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:02.4096080Z INFO      Syncing nf-core/exoseq                                     sync.py:358
2020-07-30T20:07:03.1044722Z INFO      Pipeline directory: /tmp/tmphb7smj55/exoseq                 sync.py:87
2020-07-30T20:07:03.1045541Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:03.1045932Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:03.1046282Z           github.com
2020-07-30T20:07:04.8205001Z ERROR     Sync failed for nf-core/exoseq:                            sync.py:385
2020-07-30T20:07:04.8205875Z           Workflow config variable `manifest.name` not found!
2020-07-30T20:07:04.8252982Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:04.8270716Z INFO      Syncing nf-core/gwas                                       sync.py:358
2020-07-30T20:07:05.3418299Z INFO      Pipeline directory: /tmp/tmphb7smj55/gwas                   sync.py:87
2020-07-30T20:07:05.3419586Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:05.3420005Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:05.3420410Z           github.com
2020-07-30T20:07:14.1453127Z INFO      GitHub PR created: https://github.com/nf-core/gwas/pull/3  sync.py:327
2020-07-30T20:07:14.1548183Z INFO      Sync successful for nf-core/gwas:                          sync.py:391
2020-07-30T20:07:14.1549000Z           https://github.com/nf-core/gwas/pull/3
2020-07-30T20:07:14.1619817Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:14.1633673Z INFO      Syncing nf-core/hic                                        sync.py:358
2020-07-30T20:07:14.7510849Z INFO      Pipeline directory: /tmp/tmphb7smj55/hic                    sync.py:87
2020-07-30T20:07:14.7511588Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:14.7511962Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:14.7512321Z           github.com
2020-07-30T20:07:23.8335652Z INFO      GitHub PR created: https://github.com/nf-core/hic/pull/70  sync.py:327
2020-07-30T20:07:23.8474669Z INFO      Sync successful for nf-core/hic:                           sync.py:391
2020-07-30T20:07:23.8475569Z           https://github.com/nf-core/hic/pull/70
2020-07-30T20:07:23.8538019Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:23.8552759Z INFO      Syncing nf-core/hlatyping                                  sync.py:358
2020-07-30T20:07:27.3751671Z INFO      Pipeline directory: /tmp/tmphb7smj55/hlatyping              sync.py:87
2020-07-30T20:07:27.3752354Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:27.3752695Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:27.3753202Z           github.com
2020-07-30T20:07:36.9014110Z ERROR     Sync failed for nf-core/hlatyping:                         sync.py:385
2020-07-30T20:07:36.9015517Z           GitHub API returned code 404:
2020-07-30T20:07:36.9016352Z           {
2020-07-30T20:07:36.9016710Z               "message": "Not Found",
2020-07-30T20:07:36.9017287Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:07:36.9017927Z           pulls/#create-a-pull-request"
2020-07-30T20:07:36.9018333Z           }
2020-07-30T20:07:36.9331103Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:36.9348402Z INFO      Syncing nf-core/imcyto                                     sync.py:358
2020-07-30T20:07:37.6934123Z INFO      Pipeline directory: /tmp/tmphb7smj55/imcyto                 sync.py:87
2020-07-30T20:07:37.6935253Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:37.6935634Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:37.6935934Z           github.com
2020-07-30T20:07:46.8247916Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:07:46.8249960Z           https://github.com/nf-core/imcyto/pull/35
2020-07-30T20:07:46.8445571Z INFO      Sync successful for nf-core/imcyto:                        sync.py:391
2020-07-30T20:07:46.8446345Z           https://github.com/nf-core/imcyto/pull/35
2020-07-30T20:07:46.8509605Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:46.8523612Z INFO      Syncing nf-core/kmermaid                                   sync.py:358
2020-07-30T20:07:48.9836076Z INFO      Pipeline directory: /tmp/tmphb7smj55/kmermaid               sync.py:87
2020-07-30T20:07:48.9836755Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:48.9837139Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:48.9837519Z           github.com
2020-07-30T20:07:51.3651340Z ERROR     Sync failed for nf-core/kmermaid:                          sync.py:385
2020-07-30T20:07:51.3652467Z           Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'
2020-07-30T20:07:51.3705866Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:07:51.3721868Z INFO      Syncing nf-core/lncpipe                                    sync.py:358
2020-07-30T20:07:52.0099080Z INFO      Pipeline directory: /tmp/tmphb7smj55/lncpipe                sync.py:87
2020-07-30T20:07:52.0099873Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:07:52.0100425Z             Will attempt to automatically create a pull request on
2020-07-30T20:07:52.0100802Z           github.com
2020-07-30T20:08:00.5106725Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:08:00.5107910Z           https://github.com/nf-core/lncpipe/pull/18
2020-07-30T20:08:00.5623108Z INFO      Sync successful for nf-core/lncpipe:                       sync.py:391
2020-07-30T20:08:00.5624111Z           https://github.com/nf-core/lncpipe/pull/18
2020-07-30T20:08:00.5714760Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:00.5728776Z INFO      Syncing nf-core/mag                                        sync.py:358
2020-07-30T20:08:01.3640813Z INFO      Pipeline directory: /tmp/tmphb7smj55/mag                    sync.py:87
2020-07-30T20:08:01.3641825Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:08:01.3642457Z             Will attempt to automatically create a pull request on
2020-07-30T20:08:01.3642975Z           github.com
2020-07-30T20:08:09.8053083Z ERROR     Sync failed for nf-core/mag:                               sync.py:385
2020-07-30T20:08:09.8053741Z           GitHub API returned code 404:
2020-07-30T20:08:09.8054068Z           {
2020-07-30T20:08:09.8054385Z               "message": "Not Found",
2020-07-30T20:08:09.8054727Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:08:09.8055259Z           pulls/#create-a-pull-request"
2020-07-30T20:08:09.8055618Z           }
2020-07-30T20:08:09.8122724Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:09.8143274Z INFO      Syncing nf-core/metaboigniter                              sync.py:358
2020-07-30T20:08:10.3127731Z INFO      Pipeline directory: /tmp/tmphb7smj55/metaboigniter          sync.py:87
2020-07-30T20:08:10.3128393Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:08:10.3128739Z             Will attempt to automatically create a pull request on
2020-07-30T20:08:10.3129070Z           github.com
2020-07-30T20:08:19.1974174Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:08:19.1975080Z           https://github.com/nf-core/metaboigniter/pull/2
2020-07-30T20:08:19.2103938Z INFO      Sync successful for nf-core/metaboigniter:                 sync.py:391
2020-07-30T20:08:19.2104805Z           https://github.com/nf-core/metaboigniter/pull/2
2020-07-30T20:08:19.2165147Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:19.2177357Z INFO      Syncing nf-core/methylseq                                  sync.py:358
2020-07-30T20:08:20.3220733Z INFO      Pipeline directory: /tmp/tmphb7smj55/methylseq              sync.py:87
2020-07-30T20:08:20.3221375Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:08:20.3221737Z             Will attempt to automatically create a pull request on
2020-07-30T20:08:20.3222058Z           github.com
2020-07-30T20:08:29.4279162Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:08:29.4281125Z           https://github.com/nf-core/methylseq/pull/162
2020-07-30T20:08:29.4446424Z INFO      Sync successful for nf-core/methylseq:                     sync.py:391
2020-07-30T20:08:29.4447186Z           https://github.com/nf-core/methylseq/pull/162
2020-07-30T20:08:29.4499484Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:29.4527755Z INFO      Syncing nf-core/mhcquant                                   sync.py:358
2020-07-30T20:08:30.8218011Z INFO      Pipeline directory: /tmp/tmphb7smj55/mhcquant               sync.py:87
2020-07-30T20:08:30.8218786Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:08:30.8219143Z             Will attempt to automatically create a pull request on
2020-07-30T20:08:30.8219462Z           github.com
2020-07-30T20:08:38.5980439Z ERROR     Sync failed for nf-core/mhcquant:                          sync.py:385
2020-07-30T20:08:38.5981214Z           GitHub API returned code 404:
2020-07-30T20:08:38.5981874Z           {
2020-07-30T20:08:38.5982230Z               "message": "Not Found",
2020-07-30T20:08:38.5982784Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:08:38.5983418Z           pulls/#create-a-pull-request"
2020-07-30T20:08:38.5983825Z           }
2020-07-30T20:08:38.6041195Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:38.6055453Z INFO      Syncing nf-core/mnaseseq                                   sync.py:358
2020-07-30T20:08:39.3290392Z INFO      Pipeline directory: /tmp/tmphb7smj55/mnaseseq               sync.py:87
2020-07-30T20:08:39.3291141Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:08:39.3291946Z             Will attempt to automatically create a pull request on
2020-07-30T20:08:39.3292548Z           github.com
2020-07-30T20:08:49.5998906Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:08:49.6000739Z           https://github.com/nf-core/mnaseseq/pull/16
2020-07-30T20:08:49.6167920Z INFO      Sync successful for nf-core/mnaseseq:                      sync.py:391
2020-07-30T20:08:49.6168995Z           https://github.com/nf-core/mnaseseq/pull/16
2020-07-30T20:08:49.6233496Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:49.6246087Z INFO      Syncing nf-core/nanoseq                                    sync.py:358
2020-07-30T20:08:50.3253516Z INFO      Pipeline directory: /tmp/tmphb7smj55/nanoseq                sync.py:87
2020-07-30T20:08:50.3256216Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:08:50.3256682Z             Will attempt to automatically create a pull request on
2020-07-30T20:08:50.3257018Z           github.com
2020-07-30T20:08:59.4744922Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:08:59.4746299Z           https://github.com/nf-core/nanoseq/pull/68
2020-07-30T20:08:59.4886123Z INFO      Sync successful for nf-core/nanoseq:                       sync.py:391
2020-07-30T20:08:59.4887126Z           https://github.com/nf-core/nanoseq/pull/68
2020-07-30T20:08:59.4948278Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:08:59.4965219Z INFO      Syncing nf-core/nascent                                    sync.py:358
2020-07-30T20:09:00.1818757Z INFO      Pipeline directory: /tmp/tmphb7smj55/nascent                sync.py:87
2020-07-30T20:09:00.1819609Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:09:00.1819993Z             Will attempt to automatically create a pull request on
2020-07-30T20:09:00.1820366Z           github.com
2020-07-30T20:09:08.7777444Z ERROR     Sync failed for nf-core/nascent:                           sync.py:385
2020-07-30T20:09:08.7778185Z           GitHub API returned code 404:
2020-07-30T20:09:08.7778732Z           {
2020-07-30T20:09:08.7779233Z               "message": "Not Found",
2020-07-30T20:09:08.7779612Z               "documentation_url": "https://developer.github.com/v3/
2020-07-30T20:09:08.7780205Z           pulls/#create-a-pull-request"
2020-07-30T20:09:08.7780835Z           }
2020-07-30T20:09:08.7851866Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:09:08.7867481Z INFO      Syncing nf-core/neutronstar                                sync.py:358
2020-07-30T20:09:11.6446075Z INFO      Pipeline directory: /tmp/tmphb7smj55/neutronstar            sync.py:87
2020-07-30T20:09:11.6446798Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:09:11.6447150Z             Will attempt to automatically create a pull request on
2020-07-30T20:09:11.6447466Z           github.com
2020-07-30T20:09:25.3566043Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:09:25.3567175Z           https://github.com/nf-core/neutronstar/pull/22
2020-07-30T20:09:25.4867317Z INFO      Sync successful for nf-core/neutronstar:                   sync.py:391
2020-07-30T20:09:25.4868469Z           https://github.com/nf-core/neutronstar/pull/22
2020-07-30T20:09:25.4964966Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:09:25.4979008Z INFO      Syncing nf-core/proteomicslfq                              sync.py:358
2020-07-30T20:09:26.1551463Z INFO      Pipeline directory: /tmp/tmphb7smj55/proteomicslfq          sync.py:87
2020-07-30T20:09:26.1552082Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:09:26.1552681Z             Will attempt to automatically create a pull request on
2020-07-30T20:09:26.1553058Z           github.com
2020-07-30T20:09:35.8898732Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:09:35.8900199Z           https://github.com/nf-core/proteomicslfq/pull/76
2020-07-30T20:09:35.9050106Z INFO      Sync successful for nf-core/proteomicslfq:                 sync.py:391
2020-07-30T20:09:35.9051069Z           https://github.com/nf-core/proteomicslfq/pull/76
2020-07-30T20:09:35.9121951Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:09:35.9140253Z INFO      Syncing nf-core/rnafusion                                  sync.py:358
2020-07-30T20:09:37.1937745Z INFO      Pipeline directory: /tmp/tmphb7smj55/rnafusion              sync.py:87
2020-07-30T20:09:37.1938435Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:09:37.1938965Z             Will attempt to automatically create a pull request on
2020-07-30T20:09:37.1939287Z           github.com
2020-07-30T20:09:46.7875541Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:09:46.7876943Z           https://github.com/nf-core/rnafusion/pull/155
2020-07-30T20:09:46.8033733Z INFO      Sync successful for nf-core/rnafusion:                     sync.py:391
2020-07-30T20:09:46.8034759Z           https://github.com/nf-core/rnafusion/pull/155
2020-07-30T20:09:46.8099568Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:09:46.8115473Z INFO      Syncing nf-core/rnaseq                                     sync.py:358
2020-07-30T20:09:49.1426163Z INFO      Pipeline directory: /tmp/tmphb7smj55/rnaseq                 sync.py:87
2020-07-30T20:09:49.1426783Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:09:49.1427003Z             Will attempt to automatically create a pull request on
2020-07-30T20:09:49.1427218Z           github.com
2020-07-30T20:09:58.3128604Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:09:58.3129728Z           https://github.com/nf-core/rnaseq/pull/451
2020-07-30T20:09:58.3430927Z INFO      Sync successful for nf-core/rnaseq:                        sync.py:391
2020-07-30T20:09:58.3431898Z           https://github.com/nf-core/rnaseq/pull/451
2020-07-30T20:09:58.3492183Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:09:58.3504203Z INFO      Syncing nf-core/sarek                                      sync.py:358
2020-07-30T20:09:59.2579139Z INFO      Pipeline directory: /tmp/tmphb7smj55/sarek                  sync.py:87
2020-07-30T20:09:59.2579695Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:09:59.2580030Z             Will attempt to automatically create a pull request on
2020-07-30T20:09:59.2580329Z           github.com
2020-07-30T20:10:09.9270722Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:10:09.9272042Z           https://github.com/nf-core/sarek/pull/260
2020-07-30T20:10:09.9623568Z INFO      Sync successful for nf-core/sarek:                         sync.py:391
2020-07-30T20:10:09.9624395Z           https://github.com/nf-core/sarek/pull/260
2020-07-30T20:10:09.9703305Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:10:09.9716074Z INFO      Syncing nf-core/scrnaseq                                   sync.py:358
2020-07-30T20:10:11.8338497Z INFO      Pipeline directory: /tmp/tmphb7smj55/scrnaseq               sync.py:87
2020-07-30T20:10:11.8338772Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:10:11.8338912Z             Will attempt to automatically create a pull request on
2020-07-30T20:10:11.8339069Z           github.com
2020-07-30T20:10:21.0284867Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:10:21.0286450Z           https://github.com/nf-core/scrnaseq/pull/37
2020-07-30T20:10:21.1960625Z INFO      Sync successful for nf-core/scrnaseq:                      sync.py:391
2020-07-30T20:10:21.1961165Z           https://github.com/nf-core/scrnaseq/pull/37
2020-07-30T20:10:21.2052983Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:10:21.2068175Z INFO      Syncing nf-core/slamseq                                    sync.py:358
2020-07-30T20:10:21.6618287Z INFO      Pipeline directory: /tmp/tmphb7smj55/slamseq                sync.py:87
2020-07-30T20:10:21.6618570Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:10:21.6618709Z             Will attempt to automatically create a pull request on
2020-07-30T20:10:21.6618864Z           github.com
2020-07-30T20:10:30.7224785Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:10:30.7226145Z           https://github.com/nf-core/slamseq/pull/12
2020-07-30T20:10:30.7471802Z INFO      Sync successful for nf-core/slamseq:                       sync.py:391
2020-07-30T20:10:30.7472593Z           https://github.com/nf-core/slamseq/pull/12
2020-07-30T20:10:30.7535291Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:10:30.7548191Z INFO      Syncing nf-core/smartseq2                                  sync.py:358
2020-07-30T20:10:31.3514967Z INFO      Pipeline directory: /tmp/tmphb7smj55/smartseq2              sync.py:87
2020-07-30T20:10:31.3515475Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:10:31.3515858Z             Will attempt to automatically create a pull request on
2020-07-30T20:10:31.3515986Z           github.com
2020-07-30T20:10:41.2371471Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:10:41.2372803Z           https://github.com/nf-core/smartseq2/pull/8
2020-07-30T20:10:41.2484882Z INFO      Sync successful for nf-core/smartseq2:                     sync.py:391
2020-07-30T20:10:41.2485945Z           https://github.com/nf-core/smartseq2/pull/8
2020-07-30T20:10:41.2537743Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:10:41.2550812Z INFO      Syncing nf-core/smrnaseq                                   sync.py:358
2020-07-30T20:10:41.9819111Z INFO      Pipeline directory: /tmp/tmphb7smj55/smrnaseq               sync.py:87
2020-07-30T20:10:41.9819663Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:10:41.9819902Z             Will attempt to automatically create a pull request on
2020-07-30T20:10:41.9820141Z           github.com
2020-07-30T20:10:56.2037666Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:10:56.2039081Z           https://github.com/nf-core/smrnaseq/pull/51
2020-07-30T20:10:56.2231127Z INFO      Sync successful for nf-core/smrnaseq:                      sync.py:391
2020-07-30T20:10:56.2231906Z           https://github.com/nf-core/smrnaseq/pull/51
2020-07-30T20:10:56.2289769Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:10:56.2302132Z INFO      Syncing nf-core/vipr                                       sync.py:358
2020-07-30T20:10:56.7610483Z INFO      Pipeline directory: /tmp/tmphb7smj55/vipr                   sync.py:87
2020-07-30T20:10:56.7611100Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:10:56.7611415Z             Will attempt to automatically create a pull request on
2020-07-30T20:10:56.7611706Z           github.com
2020-07-30T20:10:58.2971337Z ERROR     Sync failed for nf-core/vipr:                              sync.py:385
2020-07-30T20:10:58.2972093Z           Workflow config variable `manifest.version` not found!
2020-07-30T20:10:58.3008300Z INFO      ------------------------------                             sync.py:357
2020-07-30T20:10:58.3021096Z INFO      Syncing nf-core/viralrecon                                 sync.py:358
2020-07-30T20:10:59.2086398Z INFO      Pipeline directory: /tmp/tmphb7smj55/viralrecon             sync.py:87
2020-07-30T20:10:59.2087026Z             Using branch `dev` to fetch workflow variables
2020-07-30T20:10:59.2087416Z             Will attempt to automatically create a pull request on
2020-07-30T20:10:59.2087725Z           github.com
2020-07-30T20:11:08.9798179Z INFO      GitHub PR created:                                         sync.py:327
2020-07-30T20:11:08.9800497Z           https://github.com/nf-core/viralrecon/pull/133
2020-07-30T20:11:09.0248650Z INFO      Sync successful for nf-core/viralrecon:                    sync.py:391
2020-07-30T20:11:09.0249442Z           https://github.com/nf-core/viralrecon/pull/133
2020-07-30T20:11:09.0311160Z INFO      Finished. Successfully synchronised 31 pipelines           sync.py:403
2020-07-30T20:11:09.0339526Z ERROR     Errors whilst synchronising 12 pipelines:                  sync.py:407
2020-07-30T20:11:09.0340627Z            - ampliseq
2020-07-30T20:11:09.0341525Z            - artic
2020-07-30T20:11:09.0342135Z            - bcellmagic
2020-07-30T20:11:09.0342912Z            - clinvap
2020-07-30T20:11:09.0344875Z            - deepvariant
2020-07-30T20:11:09.0345297Z            - exoseq
2020-07-30T20:11:09.0345581Z            - hlatyping
2020-07-30T20:11:09.0345856Z            - kmermaid
2020-07-30T20:11:09.0346127Z            - mag
2020-07-30T20:11:09.0346399Z            - mhcquant
2020-07-30T20:11:09.0346685Z            - nascent
2020-07-30T20:11:09.0346955Z            - vipr

The artifact upload failed with error ##[error]read ECONNRESET
@ewels
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ewels commented Jul 30, 2020

Summary of how this went:

- ampliseq        [ PR existed ]
- artic           [ PR existed ]
+ atacseq
+ bacass
+ bactmap
- bcellmagic      [ PR existed ]
+ cageseq
+ chipseq
- clinvap         [ archived ]
+ coproid
+ crisprvar
+ ddamsproteomics
- deepvariant     [ PR error 404 ]
+ demultiplex
+ denovohybrid
+ diaproteomics
+ eager
+ epitopeprediction
- exoseq          [ archived ]
+ gwas
+ hic
- hlatyping       [ PR error 404 ]
+ imcyto
- kmermaid        [ TEMPLATE branch problem ]
+ lncpipe
- mag             [ PR error 404 ]
+ metaboigniter
+ methylseq
- mhcquant        [ PR error 404 ]
+ mnaseseq
+ nanoseq
- nascent         [ PR error 404 ]
+ neutronstar
+ proteomicslfq
+ rnafusion
+ rnaseq
+ sarek
+ scrnaseq
+ slamseq
+ smartseq2
+ smrnaseq
- vipr            [ archived ]
+ viralrecon

PR Error 422

Failure for:

  • ampliseq
  • artic
  • bcellmagic
ERROR     Sync failed for nf-core/ampliseq:                          sync.py:385
GitHub API returned code 422:
{
    "message": "Validation Failed",
    "errors": [
        {
            "resource": "PullRequest",
            "code": "custom",
            "message": "A pull request already exists for nf-core:TEMPLATE."
        }
    ],
    "documentation_url": "https://developer.github.com/v3/pulls/#create-a-pull-request"
}

This isn't really an error - a PR already exists and the new commit is just appended. We should catch these and log them properly and report them as a success / warning.

PR error 404

Failure for:

  • deepvariant
  • hlatyping
  • mag
  • mhcquant
  • nascent
ERROR     Sync failed for nf-core/deepvariant:                       sync.py:385
GitHub API returned code 404:
{
    "message": "Not Found",
    "documentation_url": "https://developer.github.com/v3/pulls/#create-a-pull-request"
}

Most worrying, as no reason for this that I can see..? Best I can think of is to try to catch them and just try again a few times with a 10 second sleep.

Problem with repo

Failure for:

  • kmermaid
ERROR     Sync failed for nf-core/kmermaid:                          sync.py:385
          Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'

Pipeline needs fixing.

Archived pipelines

Failure for:

  • clinvap
  • exoseq
  • vipr

Miscellaneous errors, but these pipelines should never have been synced because they are archived. I thought that this was fixed after the last sync (#548 (comment)) but apparently not..

This was referenced Jul 30, 2020
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@ewels
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ewels commented Nov 6, 2020

Sync worked beautifully last time, so I think we're done here.

@ewels ewels closed this as completed Nov 6, 2020
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