From c693ac3d387a5f999d967ee45d75e16819158910 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 30 Jul 2020 21:10:16 +0200
Subject: [PATCH 01/21] Fewer line breaks in PR comment

---
 .github/workflows/branch.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index b0dd5cc25a..d9b8623bec 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -24,9 +24,7 @@ jobs:
           message: |
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Beacuse of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. Beacuse of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
 

From b4284c08ee1775bb5157a36f439eaa1d9794a22a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 30 Jul 2020 21:13:07 +0200
Subject: [PATCH 02/21] Changelog updates

---
 CHANGELOG.md | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 69c9a9b2ad..2c45c9b96e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,9 +14,12 @@ Apologies for the inconvenience.
 Patch release to fix the automatic template synchronisation, which failed in the v1.10 release.
 
 * Improved logging: `nf-core --log-file log.txt` now saves a verbose log to disk.
-* GitHub actions sync now uploads verbose log as an artifact.
-* Sync - fixed several minor bugs, improved logging.
+* nf-core/tools GitHub Actions pipeline sync now uploads verbose log as an artifact.
+* Sync - fixed several minor bugs, made logging less verbose.
 * Python Rich library updated to `>=4.2.1`
+* Hopefully fix git config for pipeline sync so that commit comes from @nf-core-bot
+* Fix sync auto-PR text indentation so that it doesn't all show as code
+* Added explicit flag `--show-passed` for `nf-core lint` instead of taking logging verbosity
 
 ## [v1.10 - Copper Camel](https://github.com/nf-core/tools/releases/tag/1.10) - [2020-07-30]
 

From 4ea80de6765e26aefed07a5e4cbbf9329f0aa8f4 Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Fri, 31 Jul 2020 01:08:35 +0200
Subject: [PATCH 03/21] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c45c9b96e..c799255f67 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ Apologies for the inconvenience.
 * Fix syntax error in `/push_dockerhub.yml` GitHub Action workflow
 * Change `params.readPaths` -> `params.input_paths` in `test_full.config`
 * Check results when posting the lint results as a GitHub comment
+* Change `params.readPaths` -> `params.input_paths` in `test_full.config`
 
 ## [v1.10.1 - Copper Camel _(patch)_](https://github.com/nf-core/tools/releases/tag/1.10.1) - [2020-07-30]
 

From 7996a379f75266a68eb59ac11c8d63fe41f3cdef Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 00:15:19 +0200
Subject: [PATCH 04/21] First attempt at a dynamic matrix for sync

---
 .github/workflows/sync_test.yml | 78 +++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 .github/workflows/sync_test.yml

diff --git a/.github/workflows/sync_test.yml b/.github/workflows/sync_test.yml
new file mode 100644
index 0000000000..8cc921b717
--- /dev/null
+++ b/.github/workflows/sync_test.yml
@@ -0,0 +1,78 @@
+name: Sync matrix test
+on: [push, pull_request]
+
+jobs:
+  get-pipelines:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - id: set-matrix
+        run: |
+          curl -O https://nf-co.re/pipeline_names.json
+          echo "::set-output name=matrix::$(cat pipeline_names.json)"
+
+  sync:
+    needs: get-pipelines
+    runs-on: ubuntu-latest
+    strategy:
+      matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
+      fail-fast: false
+    steps:
+
+      - uses: actions/checkout@v2
+        name: Check out nf-core/tools
+
+      - uses: actions/checkout@v2
+        name: Check out nf-core/${{ matrix.pipeline }}
+        with:
+          repository: nf-core/${{ matrix.pipeline }}
+          ref: dev
+          token: ${{ secrets.nf_core_bot_auth_token }}
+          path: nf-core/${{ matrix.pipeline }}
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+      - name: Install Nextflow
+        run: |
+          mkdir /tmp/nextflow
+          cd /tmp/nextflow
+          wget -qO- get.nextflow.io | bash
+          sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+
+#### FOR TESTING
+      - name: Run linting
+        run: |
+          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
+            lint nf-core/${{ matrix.pipeline }}
+
+#### THE REAL THING
+#      - name: Run synchronisation
+#        if: github.repository == 'nf-core/tools'
+#        env:
+#          AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+#        run: |
+#          git config --global user.email "core@nf-co.re"
+#          git config --global user.name "nf-core-bot"
+#          nf-core --log-file sync_log.txt sync nf-core/${{ matrix.pipeline }} \
+#            --from-branch dev \
+#            --pull-request \
+#            --username nf-core-bot \
+#            --repository nf-core/${{ matrix.pipeline }} \
+#            --auth-token ${{ secrets.nf_core_bot_auth_token }}
+#########
+
+      - name: Upload sync log file artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: sync_log_${{ matrix.pipeline }}
+          path: sync_log_${{ matrix.pipeline }}.txt

From 9de0255e29d7cbe4ca686a94cefeaa5b312ad913 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 01:09:42 +0200
Subject: [PATCH 05/21] Stable new matrix sync workflow

---
 .github/workflows/sync.yml      | 40 ++++++++++++++---
 .github/workflows/sync_test.yml | 78 ---------------------------------
 2 files changed, 34 insertions(+), 84 deletions(-)
 delete mode 100644 .github/workflows/sync_test.yml

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 256a33570d..9019a20e73 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -4,13 +4,34 @@ on:
     types: [published]
 
 jobs:
-  sync-all:
-    name: Sync all pipelines
+  get-pipelines:
     runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - id: set-matrix
+        run: |
+          curl -O https://nf-co.re/pipeline_names.json
+          echo "::set-output name=matrix::$(cat pipeline_names.json)"
 
+  sync:
+    needs: get-pipelines
+    runs-on: ubuntu-latest
+    strategy:
+      matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
+      fail-fast: false
     steps:
+
       - uses: actions/checkout@v2
-        name: Check out source-code repository
+        name: Check out nf-core/tools
+
+      - uses: actions/checkout@v2
+        name: Check out nf-core/${{ matrix.pipeline }}
+        with:
+          repository: nf-core/${{ matrix.pipeline }}
+          ref: dev
+          token: ${{ secrets.nf_core_bot_auth_token }}
+          path: nf-core/${{ matrix.pipeline }}
 
       - name: Set up Python 3.8
         uses: actions/setup-python@v1
@@ -36,10 +57,17 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log.txt sync --all --username nf-core-bot --auth-token $AUTH_TOKEN
+          nf-core --log-file sync_log.txt sync nf-core/${{ matrix.pipeline }} \
+            --from-branch dev \
+            --pull-request \
+            --username nf-core-bot \
+            --repository nf-core/${{ matrix.pipeline }} \
+            --auth-token ${{ secrets.nf_core_bot_auth_token }}
+
 
       - name: Upload sync log file artifact
+        if: ${{ always() }}
         uses: actions/upload-artifact@v2
         with:
-          name: sync-log-file
-          path: sync_log.txt
+          name: sync_log_${{ matrix.pipeline }}
+          path: sync_log_${{ matrix.pipeline }}.txt
diff --git a/.github/workflows/sync_test.yml b/.github/workflows/sync_test.yml
deleted file mode 100644
index 8cc921b717..0000000000
--- a/.github/workflows/sync_test.yml
+++ /dev/null
@@ -1,78 +0,0 @@
-name: Sync matrix test
-on: [push, pull_request]
-
-jobs:
-  get-pipelines:
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.set-matrix.outputs.matrix }}
-    steps:
-      - id: set-matrix
-        run: |
-          curl -O https://nf-co.re/pipeline_names.json
-          echo "::set-output name=matrix::$(cat pipeline_names.json)"
-
-  sync:
-    needs: get-pipelines
-    runs-on: ubuntu-latest
-    strategy:
-      matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
-      fail-fast: false
-    steps:
-
-      - uses: actions/checkout@v2
-        name: Check out nf-core/tools
-
-      - uses: actions/checkout@v2
-        name: Check out nf-core/${{ matrix.pipeline }}
-        with:
-          repository: nf-core/${{ matrix.pipeline }}
-          ref: dev
-          token: ${{ secrets.nf_core_bot_auth_token }}
-          path: nf-core/${{ matrix.pipeline }}
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
-        with:
-          python-version: 3.8
-
-      - name: Install python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
-
-      - name: Install Nextflow
-        run: |
-          mkdir /tmp/nextflow
-          cd /tmp/nextflow
-          wget -qO- get.nextflow.io | bash
-          sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-
-#### FOR TESTING
-      - name: Run linting
-        run: |
-          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
-            lint nf-core/${{ matrix.pipeline }}
-
-#### THE REAL THING
-#      - name: Run synchronisation
-#        if: github.repository == 'nf-core/tools'
-#        env:
-#          AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
-#        run: |
-#          git config --global user.email "core@nf-co.re"
-#          git config --global user.name "nf-core-bot"
-#          nf-core --log-file sync_log.txt sync nf-core/${{ matrix.pipeline }} \
-#            --from-branch dev \
-#            --pull-request \
-#            --username nf-core-bot \
-#            --repository nf-core/${{ matrix.pipeline }} \
-#            --auth-token ${{ secrets.nf_core_bot_auth_token }}
-#########
-
-      - name: Upload sync log file artifact
-        if: ${{ always() }}
-        uses: actions/upload-artifact@v2
-        with:
-          name: sync_log_${{ matrix.pipeline }}
-          path: sync_log_${{ matrix.pipeline }}.txt

From d17af2b0fa0fe9118460b85c8e2834605b056bf9 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 09:14:11 +0200
Subject: [PATCH 06/21] Sync - strip out --all flag

---
 nf_core/__main__.py | 36 ++++++++----------------
 nf_core/sync.py     | 68 +--------------------------------------------
 2 files changed, 13 insertions(+), 91 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index a52b18a101..3b27daf971 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -550,14 +550,13 @@ def bump_version(pipeline_dir, new_version, nextflow):
 
 
 @nf_core_cli.command("sync", help_priority=10)
-@click.argument("pipeline_dir", type=click.Path(exists=True), nargs=-1, metavar="<pipeline directory>")
+@click.argument("pipeline_dir", required=True, type=click.Path(exists=True), metavar="<pipeline directory>")
 @click.option("-b", "--from-branch", type=str, help="The git branch to use to fetch workflow vars.")
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")
-@click.option("-u", "--username", type=str, help="GitHub username for the PR.")
-@click.option("-r", "--repository", type=str, help="GitHub repository name for the PR.")
-@click.option("-a", "--auth-token", type=str, help="GitHub API personal access token.")
-@click.option("--all", is_flag=True, default=False, help="Sync template for all nf-core pipelines.")
-def sync(pipeline_dir, from_branch, pull_request, username, repository, auth_token, all):
+@click.option("-r", "--repository", type=str, help="GitHub PR: target repository.")
+@click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
+@click.option("-a", "--auth-token", type=str, help="GitHub PR: API personal access token.")
+def sync(pipeline_dir, from_branch, pull_request, repository, username, auth_token):
     """
     Sync a pipeline TEMPLATE branch with the nf-core template.
 
@@ -571,24 +570,13 @@ def sync(pipeline_dir, from_branch, pull_request, username, repository, auth_tok
     new release of nf-core/tools (and the included template) is made.
     """
 
-    # Pull and sync all nf-core pipelines
-    if all:
-        nf_core.sync.sync_all_pipelines(username, auth_token)
-    else:
-        # Manually check for the required parameter
-        if not pipeline_dir or len(pipeline_dir) != 1:
-            log.error("Either use --all or specify one <pipeline directory>")
-            sys.exit(1)
-        else:
-            pipeline_dir = pipeline_dir[0]
-
-        # Sync the given pipeline dir
-        sync_obj = nf_core.sync.PipelineSync(pipeline_dir, from_branch, pull_request)
-        try:
-            sync_obj.sync()
-        except (nf_core.sync.SyncException, nf_core.sync.PullRequestException) as e:
-            log.error(e)
-            sys.exit(1)
+    # Sync the given pipeline dir
+    sync_obj = nf_core.sync.PipelineSync(pipeline_dir, from_branch, pull_request, repository, username, auth_token)
+    try:
+        sync_obj.sync()
+    except (nf_core.sync.SyncException, nf_core.sync.PullRequestException) as e:
+        log.error(e)
+        sys.exit(1)
 
 
 if __name__ == "__main__":
diff --git a/nf_core/sync.py b/nf_core/sync.py
index dc1fdeff56..a2d90e93cb 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -59,7 +59,7 @@ class PipelineSync(object):
     """
 
     def __init__(
-        self, pipeline_dir, from_branch=None, make_pr=False, gh_username=None, gh_repo=None, gh_auth_token=None,
+        self, pipeline_dir, from_branch=None, make_pr=False, gh_repo=None, gh_username=None, gh_auth_token=None,
     ):
         """ Initialise syncing object """
 
@@ -334,69 +334,3 @@ def reset_target_dir(self):
             self.repo.git.checkout(self.original_branch)
         except git.exc.GitCommandError as e:
             raise SyncException("Could not reset to original branch `{}`:\n{}".format(self.from_branch, e))
-
-
-def sync_all_pipelines(gh_username=None, gh_auth_token=None):
-    """Sync all nf-core pipelines
-    """
-
-    # Get remote workflows
-    wfs = nf_core.list.Workflows()
-    wfs.get_remote_workflows()
-
-    successful_syncs = []
-    failed_syncs = []
-
-    # Set up a working directory
-    tmpdir = tempfile.mkdtemp()
-
-    # Let's do some updating!
-    for wf in wfs.remote_workflows:
-
-        log.info("-" * 30)
-        log.info("Syncing {}".format(wf.full_name))
-
-        # Make a local working directory
-        wf_local_path = os.path.join(tmpdir, wf.name)
-        os.mkdir(wf_local_path)
-        log.debug("Sync working directory: {}".format(wf_local_path))
-
-        # Clone the repo
-        wf_remote_url = "https://{}@github.com/nf-core/{}".format(gh_auth_token, wf.name)
-        repo = git.Repo.clone_from(wf_remote_url, wf_local_path)
-        assert repo
-
-        # Only show error messages from pipeline creation
-        logging.getLogger("nf_core.create").setLevel(logging.ERROR)
-
-        # Sync the repo
-        log.debug("Running template sync")
-        sync_obj = nf_core.sync.PipelineSync(
-            pipeline_dir=wf_local_path,
-            from_branch="dev",
-            make_pr=True,
-            gh_username=gh_username,
-            gh_auth_token=gh_auth_token,
-        )
-        try:
-            sync_obj.sync()
-        except (SyncException, PullRequestException) as e:
-            log.error("Sync failed for {}:\n{}".format(wf.full_name, e))
-            failed_syncs.append(wf.name)
-        except Exception as e:
-            log.error("Something went wrong when syncing {}:\n{}".format(wf.full_name, e))
-            failed_syncs.append(wf.name)
-        else:
-            log.info("[green]Sync successful for {}".format(wf.full_name))
-            successful_syncs.append(wf.name)
-
-        # Clean up
-        log.debug("Removing work directory: {}".format(wf_local_path))
-        shutil.rmtree(wf_local_path)
-
-    if len(successful_syncs) > 0:
-        log.info("[green]Finished. Successfully synchronised {} pipelines".format(len(successful_syncs)))
-
-    if len(failed_syncs) > 0:
-        failed_list = "\n - ".join(failed_syncs)
-        log.error("[red]Errors whilst synchronising {} pipelines:\n - {}".format(len(failed_syncs), failed_list))

From 1ce174671d3d46579f573ee5b86c695e33ed5157 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 09:32:08 +0200
Subject: [PATCH 07/21] Sync - handle existing PR

---
 CHANGELOG.md    |  1 -
 nf_core/sync.py | 15 +++++++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c799255f67..2c45c9b96e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,6 @@ Apologies for the inconvenience.
 * Fix syntax error in `/push_dockerhub.yml` GitHub Action workflow
 * Change `params.readPaths` -> `params.input_paths` in `test_full.config`
 * Check results when posting the lint results as a GitHub comment
-* Change `params.readPaths` -> `params.input_paths` in `test_full.config`
 
 ## [v1.10.1 - Copper Camel _(patch)_](https://github.com/nf-core/tools/releases/tag/1.10.1) - [2020-07-30]
 
diff --git a/nf_core/sync.py b/nf_core/sync.py
index a2d90e93cb..2b4586710d 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -317,13 +317,20 @@ def make_pull_request(self):
             self.gh_pr_returned_data = r.content
             returned_data_prettyprint = r.content
 
-        if r.status_code != 201:
+        # PR worked
+        if r.status_code == 201:
+            log.debug("GitHub API PR worked:\n{}".format(returned_data_prettyprint))
+            log.info("GitHub PR created: {}".format(self.gh_pr_returned_data["html_url"]))
+
+        # We already had a PR open
+        elif r.status_code == 422:
+            log.warn("GitHub PR is already open!")
+
+        # Something went wrong
+        else:
             raise PullRequestException(
                 "GitHub API returned code {}: \n{}".format(r.status_code, returned_data_prettyprint)
             )
-        else:
-            log.debug("GitHub API PR worked:\n{}".format(returned_data_prettyprint))
-            log.info("GitHub PR created: {}".format(self.gh_pr_returned_data["html_url"]))
 
     def reset_target_dir(self):
         """

From 729386f0adb361dfdede54bf91f9be50647eab4d Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 09:56:24 +0200
Subject: [PATCH 08/21] Sync - check for existing PRs and update

See nf-core/tools#710
---
 nf_core/sync.py | 75 ++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 74 insertions(+), 1 deletion(-)

diff --git a/nf_core/sync.py b/nf_core/sync.py
index 2b4586710d..034460e1e7 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -287,6 +287,7 @@ def make_pull_request(self):
 
         log.debug("Submitting a pull request via the GitHub API")
 
+        pr_title = "Important! Template update for nf-core/tools v{}".format(nf_core.__version__)
         pr_body_text = (
             "A new release of the main template in nf-core/tools has just been released. "
             "This automated pull-request attempts to apply the relevant updates to this pipeline.\n\n"
@@ -298,13 +299,85 @@ def make_pull_request(self):
             "please see the [nf-core/tools v{tag} release page](https://github.com/nf-core/tools/releases/tag/{tag})."
         ).format(tag=nf_core.__version__)
 
+        # Try to update an existing pull-request
+        if self.update_existing_pull_request(pr_title, pr_body_text) is False:
+            # None found - make a new pull-request
+            self.submit_pull_request(pr_title, pr_body_text)
+
+    def update_existing_pull_request(self, pr_title, pr_body_text):
+        """
+        List existing pull-requests between TEMPLATE and self.from_branch
+
+        If one is found, attempt to update it with a new title and body text
+        If none are found, return False
+        """
+
+        # Look for existing pull-requests
+        r = requests.get(
+            url="https://api.github.com/repos/{}/{}/pulls?head=nf-core:TEMPLATE&base={}".format(
+                self.gh_username, self.gh_repo, self.from_branch
+            ),
+            auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),
+        )
+        try:
+            r_json = json.loads(r.content)
+            r_pp = json.dumps(r_json, indent=4)
+        except:
+            r_json = r.content
+            r_pp = r.content
+
+        # PR worked
+        if r.status_code == 200:
+            log.debug("GitHub API listing existing PRs:\n{}".format(r_pp))
+
+            # No open PRs
+            if len(r_json) == 0:
+                log.debug("No open PRs found between TEMPLATE and {}".format(self.from_branch))
+                return False
+
+            # Update existing PR
+            pr_update_api_url = r_json[0]["url"]
+            pr_content = {"title": pr_title, "body": pr_body_text}
+
+            r = requests.patch(
+                url=pr_update_api_url,
+                data=json.dumps(pr_content),
+                auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),
+            )
+            try:
+                r_json = json.loads(r.content)
+                r_pp = json.dumps(r_json, indent=4)
+            except:
+                r_json = r.content
+                r_pp = r.content
+
+            # PR update worked
+            if r.status_code == 200:
+                log.debug("GitHub API PR-update worked:\n{}".format(r_pp))
+                log.info("Updated GitHub PR: {}".format(r_json["html_url"]))
+                return True
+            # Something went wrong
+            else:
+                log.warn("Could not update PR {}: \n{}".format(r.status_code, r_pp))
+                return False
+
+        # Something went wrong
+        else:
+            log.warn("Could not list open PRs: \n{}".format(r.status_code, r_pp))
+            return False
+
+    def submit_pull_request(self, pr_title, pr_body_text):
+        """
+        Create a new pull-request on GitHub
+        """
         pr_content = {
-            "title": "Important! Template update for nf-core/tools v{}".format(nf_core.__version__),
+            "title": pr_title,
             "body": pr_body_text,
             "maintainer_can_modify": True,
             "head": "TEMPLATE",
             "base": self.from_branch,
         }
+
         r = requests.post(
             url="https://api.github.com/repos/{}/{}/pulls".format(self.gh_username, self.gh_repo),
             data=json.dumps(pr_content),

From 635888f3aada6863dbf01adb4a7f8b46deea910a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 10:12:38 +0200
Subject: [PATCH 09/21] Spotted a typo in the template docs

---
 .../{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md
index bd292ca180..3836aa7637 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/CONTRIBUTING.md
@@ -46,7 +46,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-: warning: Only in the unlikely and regretful event of a release happening with a bug.
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
 
 * On your own fork, make a new branch `patch` based on `upstream/master`.
 * Fix the bug, and bump version (X.Y.Z+1).

From 93c141ab6bb929f6a0b70ec1bfba762ff6a11d48 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 10:16:26 +0200
Subject: [PATCH 10/21] Remove PR-create check for existing PR

---
 nf_core/sync.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/nf_core/sync.py b/nf_core/sync.py
index 034460e1e7..5fafca2cbf 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -395,10 +395,6 @@ def submit_pull_request(self, pr_title, pr_body_text):
             log.debug("GitHub API PR worked:\n{}".format(returned_data_prettyprint))
             log.info("GitHub PR created: {}".format(self.gh_pr_returned_data["html_url"]))
 
-        # We already had a PR open
-        elif r.status_code == 422:
-            log.warn("GitHub PR is already open!")
-
         # Something went wrong
         else:
             raise PullRequestException(

From f8843649b13b571d927165010d001393830fff09 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 10:22:25 +0200
Subject: [PATCH 11/21] Test sync - check that exceptions are being triggered

---
 tests/test_sync.py | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/tests/test_sync.py b/tests/test_sync.py
index 01b56ac358..4bd3a61560 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -30,6 +30,7 @@ def test_inspect_sync_dir_notgit(self):
         psync = nf_core.sync.PipelineSync(tempfile.mkdtemp())
         try:
             psync.inspect_sync_dir()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.SyncException as e:
             assert "does not appear to be a git repository" in e.args[0]
 
@@ -42,6 +43,7 @@ def test_inspect_sync_dir_dirty(self):
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         try:
             psync.inspect_sync_dir()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.SyncException as e:
             os.remove(test_fn)
             assert e.args[0].startswith("Uncommitted changes found in pipeline directory!")
@@ -56,6 +58,7 @@ def test_get_wf_config_no_branch(self):
         try:
             psync.inspect_sync_dir()
             psync.get_wf_config()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.SyncException as e:
             assert e.args[0] == "Branch `foo` not found!"
 
@@ -82,6 +85,7 @@ def test_get_wf_config_missing_required_config(self):
         try:
             psync.inspect_sync_dir()
             psync.get_wf_config()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.SyncException as e:
             # Check that we did actually get some config back
             assert psync.wf_config["params.outdir"] == "'./results'"
@@ -163,6 +167,7 @@ def test_push_template_branch_error(self):
         # Try to push changes
         try:
             psync.push_template_branch()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.PullRequestException as e:
             assert e.args[0].startswith("Could not push TEMPLATE branch")
 
@@ -173,6 +178,7 @@ def test_make_pull_request_missing_username(self):
         psync.gh_repo = None
         try:
             psync.make_pull_request()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.PullRequestException as e:
             assert e.args[0] == "Could not find GitHub username and repo name"
 
@@ -184,6 +190,7 @@ def test_make_pull_request_missing_auth(self):
         psync.gh_auth_token = None
         try:
             psync.make_pull_request()
+            raise UserWarning("Should have hit an exception")
         except nf_core.sync.PullRequestException as e:
             assert e.args[0] == "No GitHub authentication token set - cannot make PR"
 
@@ -204,22 +211,23 @@ def __init__(self, data, status_code):
 
     @mock.patch("requests.post", side_effect=mocked_requests_post)
     def test_make_pull_request_bad_response(self, mock_post):
-        """ Try making a PR without any auth """
+        """ Try making a PR - successful response """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
-        psync.gh_username = "bad"
+        psync.gh_username = "good"
         psync.gh_repo = "response"
         psync.gh_auth_token = "test"
-        try:
-            psync.make_pull_request()
-        except nf_core.sync.PullRequestException as e:
-            assert e.args[0].startswith("GitHub API returned code 404:")
+        psync.make_pull_request()
+        assert psync.gh_pr_returned_data["html_url"] == "great_success"
 
     @mock.patch("requests.post", side_effect=mocked_requests_post)
     def test_make_pull_request_bad_response(self, mock_post):
-        """ Try making a PR without any auth """
+        """ Try making a PR and getting a 404 error """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
-        psync.gh_username = "good"
+        psync.gh_username = "bad"
         psync.gh_repo = "response"
         psync.gh_auth_token = "test"
-        psync.make_pull_request()
-        assert psync.gh_pr_returned_data["html_url"] == "great_success"
+        try:
+            psync.make_pull_request()
+            raise UserWarning("Should have hit an exception")
+        except nf_core.sync.PullRequestException as e:
+            assert e.args[0].startswith("GitHub API returned code 404:")

From 81e5c64055830cc0e8c41c4313ecc58db8a7b30e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 10:45:10 +0200
Subject: [PATCH 12/21] Sync pytests - add more tests, update

---
 nf_core/sync.py    | 12 ++++------
 tests/test_sync.py | 60 +++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 57 insertions(+), 15 deletions(-)

diff --git a/nf_core/sync.py b/nf_core/sync.py
index 5fafca2cbf..76f896f517 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -313,12 +313,10 @@ def update_existing_pull_request(self, pr_title, pr_body_text):
         """
 
         # Look for existing pull-requests
-        r = requests.get(
-            url="https://api.github.com/repos/{}/{}/pulls?head=nf-core:TEMPLATE&base={}".format(
-                self.gh_username, self.gh_repo, self.from_branch
-            ),
-            auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),
+        list_prs_url = "https://api.github.com/repos/{}/{}/pulls?head=nf-core:TEMPLATE&base={}".format(
+            self.gh_username, self.gh_repo, self.from_branch
         )
+        r = requests.get(url=list_prs_url, auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),)
         try:
             r_json = json.loads(r.content)
             r_pp = json.dumps(r_json, indent=4)
@@ -358,12 +356,12 @@ def update_existing_pull_request(self, pr_title, pr_body_text):
                 return True
             # Something went wrong
             else:
-                log.warn("Could not update PR {}: \n{}".format(r.status_code, r_pp))
+                log.warn("Could not update PR ('{}'):\n{}\n{}".format(r.status_code, pr_update_api_url, r_pp))
                 return False
 
         # Something went wrong
         else:
-            log.warn("Could not list open PRs: \n{}".format(r.status_code, r_pp))
+            log.warn("Could not list open PRs ('{}')\n{}\n{}".format(r.status_code, list_prs_url, r_pp))
             return False
 
     def submit_pull_request(self, pr_title, pr_body_text):
diff --git a/tests/test_sync.py b/tests/test_sync.py
index 4bd3a61560..357c3a479e 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -194,7 +194,7 @@ def test_make_pull_request_missing_auth(self):
         except nf_core.sync.PullRequestException as e:
             assert e.args[0] == "No GitHub authentication token set - cannot make PR"
 
-    def mocked_requests_post(**kwargs):
+    def mocked_requests_get(**kwargs):
         """ Helper function to emulate POST requests responses from the web """
 
         class MockResponse:
@@ -202,28 +202,62 @@ def __init__(self, data, status_code):
                 self.status_code = status_code
                 self.content = json.dumps(data)
 
-        if kwargs["url"] == "https://api.github.com/repos/bad/response/pulls":
-            return MockResponse({}, 404)
+        url_template = "https://api.github.com/repos/{}/response/pulls?head=nf-core:TEMPLATE&base=None"
+        if kwargs["url"] == url_template.format("no_existing_pr"):
+            response_data = []
+            return MockResponse(response_data, 200)
+
+        if kwargs["url"] == url_template.format("existing_pr"):
+            response_data = [{"url": "url_to_update_pr"}]
+            return MockResponse(response_data, 200)
+
+        return MockResponse({"get_url": kwargs["url"]}, 404)
+
+    def mocked_requests_patch(**kwargs):
+        """ Helper function to emulate POST requests responses from the web """
+
+        class MockResponse:
+            def __init__(self, data, status_code):
+                self.status_code = status_code
+                self.content = json.dumps(data)
+
+        if kwargs["url"] == "url_to_update_pr":
+            response_data = {"html_url": "great_success"}
+            return MockResponse(response_data, 200)
+
+        return MockResponse({"patch_url": kwargs["url"]}, 404)
 
-        if kwargs["url"] == "https://api.github.com/repos/good/response/pulls":
+    def mocked_requests_post(**kwargs):
+        """ Helper function to emulate POST requests responses from the web """
+
+        class MockResponse:
+            def __init__(self, data, status_code):
+                self.status_code = status_code
+                self.content = json.dumps(data)
+
+        if kwargs["url"] == "https://api.github.com/repos/no_existing_pr/response/pulls":
             response_data = {"html_url": "great_success"}
             return MockResponse(response_data, 201)
 
+        return MockResponse({"post_url": kwargs["url"]}, 404)
+
+    @mock.patch("requests.get", side_effect=mocked_requests_get)
     @mock.patch("requests.post", side_effect=mocked_requests_post)
-    def test_make_pull_request_bad_response(self, mock_post):
+    def test_make_pull_request_success(self, mock_get, mock_post):
         """ Try making a PR - successful response """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
-        psync.gh_username = "good"
+        psync.gh_username = "no_existing_pr"
         psync.gh_repo = "response"
         psync.gh_auth_token = "test"
         psync.make_pull_request()
         assert psync.gh_pr_returned_data["html_url"] == "great_success"
 
+    @mock.patch("requests.get", side_effect=mocked_requests_get)
     @mock.patch("requests.post", side_effect=mocked_requests_post)
-    def test_make_pull_request_bad_response(self, mock_post):
+    def test_make_pull_request_bad_response(self, mock_get, mock_post):
         """ Try making a PR and getting a 404 error """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
-        psync.gh_username = "bad"
+        psync.gh_username = "bad_url"
         psync.gh_repo = "response"
         psync.gh_auth_token = "test"
         try:
@@ -231,3 +265,13 @@ def test_make_pull_request_bad_response(self, mock_post):
             raise UserWarning("Should have hit an exception")
         except nf_core.sync.PullRequestException as e:
             assert e.args[0].startswith("GitHub API returned code 404:")
+
+    @mock.patch("requests.get", side_effect=mocked_requests_get)
+    @mock.patch("requests.patch", side_effect=mocked_requests_patch)
+    def test_update_existing_pull_request(self, mock_get, mock_patch):
+        """ Try discovering a PR and updating it """
+        psync = nf_core.sync.PipelineSync(self.pipeline_dir)
+        psync.gh_username = "existing_pr"
+        psync.gh_repo = "response"
+        psync.gh_auth_token = "test"
+        assert psync.update_existing_pull_request("title", "body") is True

From 40ad562e1d1703a9bbb028c64f38df60f925e0b7 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 10:58:29 +0200
Subject: [PATCH 13/21] Sync - use env variable for auth token instead of cli
 argument

---
 .github/workflows/sync.yml |  5 ++---
 nf_core/__main__.py        |  3 +--
 nf_core/sync.py            | 20 ++++++++++----------
 3 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 9019a20e73..5baa78de7c 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -53,7 +53,7 @@ jobs:
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'
         env:
-          AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+          GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
@@ -61,8 +61,7 @@ jobs:
             --from-branch dev \
             --pull-request \
             --username nf-core-bot \
-            --repository nf-core/${{ matrix.pipeline }} \
-            --auth-token ${{ secrets.nf_core_bot_auth_token }}
+            --repository nf-core/${{ matrix.pipeline }}
 
 
       - name: Upload sync log file artifact
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 3b27daf971..4abea69788 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -555,7 +555,6 @@ def bump_version(pipeline_dir, new_version, nextflow):
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")
 @click.option("-r", "--repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
-@click.option("-a", "--auth-token", type=str, help="GitHub PR: API personal access token.")
 def sync(pipeline_dir, from_branch, pull_request, repository, username, auth_token):
     """
     Sync a pipeline TEMPLATE branch with the nf-core template.
@@ -571,7 +570,7 @@ def sync(pipeline_dir, from_branch, pull_request, repository, username, auth_tok
     """
 
     # Sync the given pipeline dir
-    sync_obj = nf_core.sync.PipelineSync(pipeline_dir, from_branch, pull_request, repository, username, auth_token)
+    sync_obj = nf_core.sync.PipelineSync(pipeline_dir, from_branch, pull_request, repository, username)
     try:
         sync_obj.sync()
     except (nf_core.sync.SyncException, nf_core.sync.PullRequestException) as e:
diff --git a/nf_core/sync.py b/nf_core/sync.py
index 76f896f517..eac1db484f 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -44,7 +44,6 @@ class PipelineSync(object):
         make_pr (bool): Set this to `True` to create a GitHub pull-request with the changes
         gh_username (str): GitHub username
         gh_repo (str): GitHub repository name
-        gh_auth_token (str): Authorisation token used to make PR with GitHub API
 
     Attributes:
         pipeline_dir (str): Path to target pipeline directory
@@ -55,11 +54,10 @@ class PipelineSync(object):
         required_config_vars (list): List of nextflow variables required to make template pipeline
         gh_username (str): GitHub username
         gh_repo (str): GitHub repository name
-        gh_auth_token (str): Authorisation token used to make PR with GitHub API
     """
 
     def __init__(
-        self, pipeline_dir, from_branch=None, make_pr=False, gh_repo=None, gh_username=None, gh_auth_token=None,
+        self, pipeline_dir, from_branch=None, make_pr=False, gh_repo=None, gh_username=None,
     ):
         """ Initialise syncing object """
 
@@ -73,7 +71,6 @@ def __init__(
 
         self.gh_username = gh_username
         self.gh_repo = gh_repo
-        self.gh_auth_token = gh_auth_token
 
     def sync(self):
         """ Find workflow attributes, create a new template pipeline on TEMPLATE
@@ -276,14 +273,14 @@ def make_pull_request(self):
 
         # If we've been asked to make a PR, check that we have the credentials
         try:
-            assert self.gh_auth_token is not None
+            assert os.environ.get("GITHUB_AUTH_TOKEN", "") != ""
         except AssertionError:
             log.info(
                 "Make a PR at the following URL:\n  https://github.com/{}/{}/compare/{}...TEMPLATE".format(
                     self.gh_username, self.gh_repo, self.original_branch
                 )
             )
-            raise PullRequestException("No GitHub authentication token set - cannot make PR")
+            raise PullRequestException("Environment variable GITHUB_AUTH_TOKEN not set - cannot make PR")
 
         log.debug("Submitting a pull request via the GitHub API")
 
@@ -311,12 +308,14 @@ def update_existing_pull_request(self, pr_title, pr_body_text):
         If one is found, attempt to update it with a new title and body text
         If none are found, return False
         """
-
+        assert os.environ.get("GITHUB_AUTH_TOKEN", "") != ""
         # Look for existing pull-requests
         list_prs_url = "https://api.github.com/repos/{}/{}/pulls?head=nf-core:TEMPLATE&base={}".format(
             self.gh_username, self.gh_repo, self.from_branch
         )
-        r = requests.get(url=list_prs_url, auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),)
+        r = requests.get(
+            url=list_prs_url, auth=requests.auth.HTTPBasicAuth(self.gh_username, os.environ.get("GITHUB_AUTH_TOKEN")),
+        )
         try:
             r_json = json.loads(r.content)
             r_pp = json.dumps(r_json, indent=4)
@@ -340,7 +339,7 @@ def update_existing_pull_request(self, pr_title, pr_body_text):
             r = requests.patch(
                 url=pr_update_api_url,
                 data=json.dumps(pr_content),
-                auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),
+                auth=requests.auth.HTTPBasicAuth(self.gh_username, os.environ.get("GITHUB_AUTH_TOKEN")),
             )
             try:
                 r_json = json.loads(r.content)
@@ -368,6 +367,7 @@ def submit_pull_request(self, pr_title, pr_body_text):
         """
         Create a new pull-request on GitHub
         """
+        assert os.environ.get("GITHUB_AUTH_TOKEN", "") != ""
         pr_content = {
             "title": pr_title,
             "body": pr_body_text,
@@ -379,7 +379,7 @@ def submit_pull_request(self, pr_title, pr_body_text):
         r = requests.post(
             url="https://api.github.com/repos/{}/{}/pulls".format(self.gh_username, self.gh_repo),
             data=json.dumps(pr_content),
-            auth=requests.auth.HTTPBasicAuth(self.gh_username, self.gh_auth_token),
+            auth=requests.auth.HTTPBasicAuth(self.gh_username, os.environ.get("GITHUB_AUTH_TOKEN")),
         )
         try:
             self.gh_pr_returned_data = json.loads(r.content)

From 240f9da0ed3d0c160dab695faf1379bdcc392b6a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:14:17 +0200
Subject: [PATCH 14/21] Make lots of log message INFO again

---
 nf_core/__main__.py |  2 +-
 nf_core/sync.py     | 28 ++++++++++++++--------------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 4abea69788..be9bdfaac9 100755
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -555,7 +555,7 @@ def bump_version(pipeline_dir, new_version, nextflow):
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")
 @click.option("-r", "--repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
-def sync(pipeline_dir, from_branch, pull_request, repository, username, auth_token):
+def sync(pipeline_dir, from_branch, pull_request, repository, username):
     """
     Sync a pipeline TEMPLATE branch with the nf-core template.
 
diff --git a/nf_core/sync.py b/nf_core/sync.py
index eac1db484f..3e7a897659 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -76,11 +76,11 @@ def sync(self):
         """ Find workflow attributes, create a new template pipeline on TEMPLATE
         """
 
-        log.debug("Pipeline directory: {}".format(self.pipeline_dir))
+        log.info("Pipeline directory: {}".format(self.pipeline_dir))
         if self.from_branch:
-            log.debug("Using branch `{}` to fetch workflow variables".format(self.from_branch))
+            log.info("Using branch `{}` to fetch workflow variables".format(self.from_branch))
         if self.make_pr:
-            log.debug("Will attempt to automatically create a pull request")
+            log.info("Will attempt to automatically create a pull request")
 
         self.inspect_sync_dir()
         self.get_wf_config()
@@ -121,7 +121,7 @@ def inspect_sync_dir(self):
 
         # get current branch so we can switch back later
         self.original_branch = self.repo.active_branch.name
-        log.debug("Original pipeline repository branch is '{}'".format(self.original_branch))
+        log.info("Original pipeline repository branch is '{}'".format(self.original_branch))
 
         # Check to see if there are uncommitted changes on current branch
         if self.repo.is_dirty(untracked_files=True):
@@ -136,7 +136,7 @@ def get_wf_config(self):
         # Try to check out target branch (eg. `origin/dev`)
         try:
             if self.from_branch and self.repo.active_branch.name != self.from_branch:
-                log.debug("Checking out workflow branch '{}'".format(self.from_branch))
+                log.info("Checking out workflow branch '{}'".format(self.from_branch))
                 self.repo.git.checkout(self.from_branch)
         except git.exc.GitCommandError:
             raise SyncException("Branch `{}` not found!".format(self.from_branch))
@@ -197,7 +197,7 @@ def delete_template_branch_files(self):
         Delete all files in the TEMPLATE branch
         """
         # Delete everything
-        log.debug("Deleting all files in TEMPLATE branch")
+        log.info("Deleting all files in TEMPLATE branch")
         for the_file in os.listdir(self.pipeline_dir):
             if the_file == ".git":
                 continue
@@ -215,7 +215,7 @@ def make_template_pipeline(self):
         """
         Delete all files and make a fresh template using the workflow variables
         """
-        log.debug("Making a new template pipeline using pipeline variables")
+        log.info("Making a new template pipeline using pipeline variables")
 
         # Only show error messages from pipeline creation
         logging.getLogger("nf_core.create").setLevel(logging.ERROR)
@@ -242,7 +242,7 @@ def commit_template_changes(self):
             self.repo.git.add(A=True)
             self.repo.index.commit("Template update for nf-core/tools version {}".format(nf_core.__version__))
             self.made_changes = True
-            log.debug("Committed changes to TEMPLATE branch")
+            log.info("Committed changes to TEMPLATE branch")
         except Exception as e:
             raise SyncException("Could not commit changes to TEMPLATE:\n{}".format(e))
         return True
@@ -252,7 +252,7 @@ def push_template_branch(self):
         and try to make a PR. If we don't have the auth token, try to figure out a URL
         for the PR and print this to the console.
         """
-        log.debug("Pushing TEMPLATE branch to remote: '{}'".format(os.path.basename(self.pipeline_dir)))
+        log.info("Pushing TEMPLATE branch to remote: '{}'".format(os.path.basename(self.pipeline_dir)))
         try:
             self.repo.git.push()
         except git.exc.GitCommandError as e:
@@ -275,14 +275,14 @@ def make_pull_request(self):
         try:
             assert os.environ.get("GITHUB_AUTH_TOKEN", "") != ""
         except AssertionError:
-            log.info(
+            raise PullRequestException(
+                "Environment variable GITHUB_AUTH_TOKEN not set - cannot make PR\n"
                 "Make a PR at the following URL:\n  https://github.com/{}/{}/compare/{}...TEMPLATE".format(
                     self.gh_username, self.gh_repo, self.original_branch
                 )
             )
-            raise PullRequestException("Environment variable GITHUB_AUTH_TOKEN not set - cannot make PR")
 
-        log.debug("Submitting a pull request via the GitHub API")
+        log.info("Submitting a pull request via the GitHub API")
 
         pr_title = "Important! Template update for nf-core/tools v{}".format(nf_core.__version__)
         pr_body_text = (
@@ -329,7 +329,7 @@ def update_existing_pull_request(self, pr_title, pr_body_text):
 
             # No open PRs
             if len(r_json) == 0:
-                log.debug("No open PRs found between TEMPLATE and {}".format(self.from_branch))
+                log.info("No open PRs found between TEMPLATE and {}".format(self.from_branch))
                 return False
 
             # Update existing PR
@@ -403,7 +403,7 @@ def reset_target_dir(self):
         """
         Reset the target pipeline directory. Check out the original branch.
         """
-        log.debug("Checking out original branch: '{}'".format(self.original_branch))
+        log.info("Checking out original branch: '{}'".format(self.original_branch))
         try:
             self.repo.git.checkout(self.original_branch)
         except git.exc.GitCommandError as e:

From 75d7238af93c4246683931c572c900f6df18d71e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:20:40 +0200
Subject: [PATCH 15/21] Sync pytests - update to work with env var auth

---
 tests/test_sync.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/tests/test_sync.py b/tests/test_sync.py
index 357c3a479e..d674bcad8d 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -187,12 +187,16 @@ def test_make_pull_request_missing_auth(self):
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "foo"
         psync.gh_repo = "bar"
-        psync.gh_auth_token = None
+        if "GITHUB_AUTH_TOKEN" in os.environ:
+            del os.environ["GITHUB_AUTH_TOKEN"]
         try:
             psync.make_pull_request()
             raise UserWarning("Should have hit an exception")
         except nf_core.sync.PullRequestException as e:
-            assert e.args[0] == "No GitHub authentication token set - cannot make PR"
+            assert e.args[0] == (
+                "Environment variable GITHUB_AUTH_TOKEN not set - cannot make PR\n"
+                "Make a PR at the following URL:\n  https://github.com/foo/bar/compare/None...TEMPLATE"
+            )
 
     def mocked_requests_get(**kwargs):
         """ Helper function to emulate POST requests responses from the web """
@@ -248,7 +252,7 @@ def test_make_pull_request_success(self, mock_get, mock_post):
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "no_existing_pr"
         psync.gh_repo = "response"
-        psync.gh_auth_token = "test"
+        os.environ["GITHUB_AUTH_TOKEN"] = "test"
         psync.make_pull_request()
         assert psync.gh_pr_returned_data["html_url"] == "great_success"
 
@@ -259,7 +263,7 @@ def test_make_pull_request_bad_response(self, mock_get, mock_post):
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "bad_url"
         psync.gh_repo = "response"
-        psync.gh_auth_token = "test"
+        os.environ["GITHUB_AUTH_TOKEN"] = "test"
         try:
             psync.make_pull_request()
             raise UserWarning("Should have hit an exception")
@@ -273,5 +277,5 @@ def test_update_existing_pull_request(self, mock_get, mock_patch):
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "existing_pr"
         psync.gh_repo = "response"
-        psync.gh_auth_token = "test"
+        os.environ["GITHUB_AUTH_TOKEN"] = "test"
         assert psync.update_existing_pull_request("title", "body") is True

From 777e115253ce2964a0c2e48a81c5f5d575702715 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:23:12 +0200
Subject: [PATCH 16/21] Sync log file - correct filename

---
 .github/workflows/sync.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 5baa78de7c..764649e5cc 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -57,7 +57,7 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log.txt sync nf-core/${{ matrix.pipeline }} \
+          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt sync nf-core/${{ matrix.pipeline }} \
             --from-branch dev \
             --pull-request \
             --username nf-core-bot \

From 866a591fbf50f71166439874c8f014a81dcd0f97 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:24:47 +0200
Subject: [PATCH 17/21] Add comment to actions yaml for branch protection
 comments

---
 .../{{cookiecutter.name_noslash}}/.github/workflows/branch.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
index 94ec0a87ca..a561ad54f0 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/workflows/branch.yml
@@ -17,6 +17,7 @@ jobs:
 
 {% raw %}
       # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
         uses: mshick/add-pr-comment@v1

From 7aed3bc60fa4d7852de27990abf12aac3939ade2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:39:17 +0200
Subject: [PATCH 18/21] Sync - don't be clever and try to figure out the remote
 repo name automatically

---
 nf_core/sync.py    | 20 --------------------
 tests/test_sync.py | 15 ---------------
 2 files changed, 35 deletions(-)

diff --git a/nf_core/sync.py b/nf_core/sync.py
index 3e7a897659..8bc2e8c2ff 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -148,26 +148,6 @@ def get_wf_config(self):
             except git.exc.GitCommandError as e:
                 log.error("Could not find active repo branch: ".format(e))
 
-        # Figure out the GitHub username and repo name from the 'origin' remote if we can
-        try:
-            origin_url = self.repo.remotes.origin.url.rstrip(".git")
-            gh_origin_match = re.search(r"github\.com[:\/]([^\/]+)/([^\/]+)$", origin_url)
-            if gh_origin_match:
-                self.gh_username = gh_origin_match.group(1)
-                self.gh_repo = gh_origin_match.group(2)
-            else:
-                raise AttributeError
-        except AttributeError as e:
-            log.debug(
-                "Could not find repository URL for remote called 'origin' from remote: {}".format(self.repo.remotes)
-            )
-        else:
-            log.debug(
-                "Found username and repo from remote: {}, {} - {}".format(
-                    self.gh_username, self.gh_repo, self.repo.remotes.origin.url
-                )
-            )
-
         # Fetch workflow variables
         log.debug("Fetching workflow config variables")
         self.wf_config = nf_core.utils.fetch_wf_config(self.pipeline_dir)
diff --git a/tests/test_sync.py b/tests/test_sync.py
index d674bcad8d..089271aba7 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -62,21 +62,6 @@ def test_get_wf_config_no_branch(self):
         except nf_core.sync.SyncException as e:
             assert e.args[0] == "Branch `foo` not found!"
 
-    def test_get_wf_config_fetch_origin(self):
-        """
-        Try getting the GitHub username and repo from the git origin
-
-        Also checks the fetched config variables, should pass
-        """
-        # Try to sync, check we halt with the right error
-        psync = nf_core.sync.PipelineSync(self.pipeline_dir)
-        psync.inspect_sync_dir()
-        # Add a remote to the git repo
-        psync.repo.create_remote("origin", "https://github.com/nf-core/demo.git")
-        psync.get_wf_config()
-        assert psync.gh_username == "nf-core"
-        assert psync.gh_repo == "demo"
-
     def test_get_wf_config_missing_required_config(self):
         """ Try getting a workflow config, then make it miss a required config option """
         # Try to sync, check we halt with the right error

From fa834a35cd5b839371d47b0f312d187b509d6549 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:42:20 +0200
Subject: [PATCH 19/21] Fix the now-broken URLs for the GitHub API

---
 nf_core/sync.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nf_core/sync.py b/nf_core/sync.py
index 8bc2e8c2ff..0f48eb5161 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -257,8 +257,8 @@ def make_pull_request(self):
         except AssertionError:
             raise PullRequestException(
                 "Environment variable GITHUB_AUTH_TOKEN not set - cannot make PR\n"
-                "Make a PR at the following URL:\n  https://github.com/{}/{}/compare/{}...TEMPLATE".format(
-                    self.gh_username, self.gh_repo, self.original_branch
+                "Make a PR at the following URL:\n  https://github.com/{}/compare/{}...TEMPLATE".format(
+                    self.gh_repo, self.original_branch
                 )
             )
 
@@ -290,8 +290,8 @@ def update_existing_pull_request(self, pr_title, pr_body_text):
         """
         assert os.environ.get("GITHUB_AUTH_TOKEN", "") != ""
         # Look for existing pull-requests
-        list_prs_url = "https://api.github.com/repos/{}/{}/pulls?head=nf-core:TEMPLATE&base={}".format(
-            self.gh_username, self.gh_repo, self.from_branch
+        list_prs_url = "https://api.github.com/repos/{}/pulls?head=nf-core:TEMPLATE&base={}".format(
+            self.gh_repo, self.from_branch
         )
         r = requests.get(
             url=list_prs_url, auth=requests.auth.HTTPBasicAuth(self.gh_username, os.environ.get("GITHUB_AUTH_TOKEN")),
@@ -357,7 +357,7 @@ def submit_pull_request(self, pr_title, pr_body_text):
         }
 
         r = requests.post(
-            url="https://api.github.com/repos/{}/{}/pulls".format(self.gh_username, self.gh_repo),
+            url="https://api.github.com/repos/{}/pulls".format(self.gh_repo),
             data=json.dumps(pr_content),
             auth=requests.auth.HTTPBasicAuth(self.gh_username, os.environ.get("GITHUB_AUTH_TOKEN")),
         )

From 0d2da051934a110e19e65e1d6fd0c93990237409 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 11:48:14 +0200
Subject: [PATCH 20/21] Changelog update

---
 CHANGELOG.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c45c9b96e..2fcf3628f8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,13 @@ Apologies for the inconvenience.
 * Fix syntax error in `/push_dockerhub.yml` GitHub Action workflow
 * Change `params.readPaths` -> `params.input_paths` in `test_full.config`
 * Check results when posting the lint results as a GitHub comment
+  * This feature is unfortunately not possible when making PRs from forks outside of the nf-core organisation for now.
+* More major refactoring of the automated pipeline sync
+  * New GitHub Actions matrix parallelisation of sync jobs across pipelines [[#673](https://github.com/nf-core/tools/issues/673)]
+  * Removed the `--all` behaviour from `nf-core sync` as we no longer need it
+  * Sync now uses a new list of pipelines on the website which does not include archived pipelines [[#712](https://github.com/nf-core/tools/issues/712)]
+  * When making a PR it checks if a PR already exists - if so it updates it [[#710](https://github.com/nf-core/tools/issues/710)]
+  * More tests and code refactoring for more stable code. Hopefully fixes 404 error [[#711](https://github.com/nf-core/tools/issues/711)]
 
 ## [v1.10.1 - Copper Camel _(patch)_](https://github.com/nf-core/tools/releases/tag/1.10.1) - [2020-07-30]
 

From ee5c0109774a51de0094e973338bcc17df32f36e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 31 Jul 2020 12:06:39 +0200
Subject: [PATCH 21/21] Update tests to use proper gh_repo style

---
 tests/test_sync.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_sync.py b/tests/test_sync.py
index 089271aba7..c7726cfb7d 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -171,7 +171,7 @@ def test_make_pull_request_missing_auth(self):
         """ Try making a PR without any auth """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "foo"
-        psync.gh_repo = "bar"
+        psync.gh_repo = "foo/bar"
         if "GITHUB_AUTH_TOKEN" in os.environ:
             del os.environ["GITHUB_AUTH_TOKEN"]
         try:
@@ -236,7 +236,7 @@ def test_make_pull_request_success(self, mock_get, mock_post):
         """ Try making a PR - successful response """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "no_existing_pr"
-        psync.gh_repo = "response"
+        psync.gh_repo = "no_existing_pr/response"
         os.environ["GITHUB_AUTH_TOKEN"] = "test"
         psync.make_pull_request()
         assert psync.gh_pr_returned_data["html_url"] == "great_success"
@@ -247,7 +247,7 @@ def test_make_pull_request_bad_response(self, mock_get, mock_post):
         """ Try making a PR and getting a 404 error """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "bad_url"
-        psync.gh_repo = "response"
+        psync.gh_repo = "bad_url/response"
         os.environ["GITHUB_AUTH_TOKEN"] = "test"
         try:
             psync.make_pull_request()
@@ -261,6 +261,6 @@ def test_update_existing_pull_request(self, mock_get, mock_patch):
         """ Try discovering a PR and updating it """
         psync = nf_core.sync.PipelineSync(self.pipeline_dir)
         psync.gh_username = "existing_pr"
-        psync.gh_repo = "response"
+        psync.gh_repo = "existing_pr/response"
         os.environ["GITHUB_AUTH_TOKEN"] = "test"
         assert psync.update_existing_pull_request("title", "body") is True