Merge branch 'master' into rpetit3-print-choices

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,42 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Hi there!
+
+        Thanks for telling us about a problem with the nf-core/tools package.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command and output from your terminal.
+      render: console
+      placeholder: |
+        $ nf-core lint ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.04.01)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
+        * Python version _(eg. 3.7, 3.8)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,3 @@
-blank_issues_enabled: false
 contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for nf-core/tools
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/workflows/create-lint-wf.yml

@@ -1,12 +1,15 @@
 name: Create a pipeline and lint it
 on: [push, pull_request]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
   MakeTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and latest edge version
+        nxf_ver: ["NXF_VER=21.04.0", "NXF_EDGE=1"]
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -27,6 +30,8 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+          export ${{ matrix.nxf_ver }}
+          nextflow self-update
 
       - name: nf-core create
         run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"

.github/workflows/create-test-wf.yml

@@ -1,12 +1,15 @@
 name: Create a pipeline and test it
 on: [push, pull_request]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
   RunTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and latest edge version
+        nxf_ver: ["NXF_VER=21.04.0", "NXF_EDGE=1"]
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -27,6 +30,8 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+          export ${{ matrix.nxf_ver }}
+          nextflow self-update
 
       - name: Run nf-core/tools
         run: |

.github/workflows/python-lint.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Check code lints with Black
-        uses: jpetrucciani/black-check@master
+        uses: psf/black@stable
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment

CHANGELOG.md

@@ -1,5 +1,32 @@
 # nf-core/tools: Changelog
 
+## v2.2dev
+
+### Template
+
+* Disable cache in `nf_core.utils.fetch_wf_config` while performing `test_wf_use_local_configs`.
+* Modify software version channel handling to support multiple software version emissions (e.g. from mulled containers), and multiple software versions.
+* Update `dumpsoftwareversion` module to correctly report versions with trailing zeros.
+* Remove `params.hostnames` from the pipeline template ([#1304](https://github.com/nf-core/tools/issues/1304))
+* Update `.gitattributes` to mark installed modules and subworkflows as `linguist-generated` ([#1311](https://github.com/nf-core/tools/issues/1311))
+* New YAML issue templates for pipeline bug reports and feature requests, with a much richer interface ([#1165](https://github.com/nf-core/tools/pull/1165))
+
+### General
+
+* Changed `questionary` `ask()` to `unsafe_ask()` to not catch `KeyboardInterupts` ([#1237](https://github.com/nf-core/tools/issues/1237))
+* Fixed bug in `nf-core launch` due to revisions specified with `-r` not being added to nextflow command. ([#1246](https://github.com/nf-core/tools/issues/1246))
+* Update regex in `readme` test of `nf-core lint` to agree with the pipeline template ([#1260](https://github.com/nf-core/tools/issues/1260))
+* Update 'fix' message in `nf-core lint` to conform to the current command line options. ([#1259](https://github.com/nf-core/tools/issues/1259))
+* Fixed bug in `nf-core list` when `NXF_HOME` is set
+* Run CI test used to create and lint/run the pipeline template with minimum and latest edge release of NF ([#1304](https://github.com/nf-core/tools/issues/1304))
+* New YAML issue templates for tools bug reports and feature requests, with a much richer interface ([#1165](https://github.com/nf-core/tools/pull/1165))
+
+### Modules
+
+* Fixed typo in `module_utils.py`.
+* Added `--diff` flag to `nf-core modules update` which shows the diff between the installed files and the versions
+* Update `nf-core modules create` help texts which were not changed with the introduction of the `--dir` flag
+
 ## [v2.1 - Zinc Zebra](https://github.com/nf-core/tools/releases/tag/2.1) - [2021-07-27]
 
 ### Template

README.md

@@ -1019,11 +1019,12 @@ INFO     Downloaded 3 files to ./modules/nf-core/modules/fastqc
 
 You can pass the module name as an optional argument to `nf-core modules update` instead of using the cli prompt, eg: `nf-core modules update fastqc`. You can specify a pipeline directory other than the current working directory by using the `--dir <pipeline dir>`.
 
-There are four additional flags that you can use with this command:
+There are five additional flags that you can use with this command:
 
 * `--force`: Reinstall module even if it appears to be up to date
 * `--prompt`: Select the module version using a cli prompt.
 * `--sha <commit_sha>`: Install the module at a specific commit from the `nf-core/modules` repository.
+* `--diff`: Show the diff between the installed files and the new version before installing.
 * `--all`: Use this flag to run the command on all modules in the pipeline.
 
 If you don't want to update certain modules or want to update them to specific versions, you can make use of the `.nf-core.yml` configuration file. For example, you can prevent the `star/align` module installed from `nf-core/modules` from being updated by adding the following to the `.nf-core.yml` file:

nf_core/__main__.py

@@ -449,14 +449,19 @@ def install(ctx, tool, dir, prompt, force, sha):
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
 @click.option("-a", "--all", is_flag=True, default=False, help="Update all modules installed in pipeline")
-def update(ctx, tool, dir, force, prompt, sha, all):
+@click.option(
+    "-c", "--diff", is_flag=True, default=False, help="Show differences between module versions before updating"
+)
+def update(ctx, tool, dir, force, prompt, sha, all, diff):
     """
     Update DSL2 modules within a pipeline.
 
     Fetches and updates module files from a remote repo e.g. nf-core/modules.
     """
     try:
-        module_install = nf_core.modules.ModuleUpdate(dir, force=force, prompt=prompt, sha=sha, update_all=all)
+        module_install = nf_core.modules.ModuleUpdate(
+            dir, force=force, prompt=prompt, sha=sha, update_all=all, diff=diff
+        )
         module_install.modules_repo = ctx.obj["modules_repo_obj"]
         exit_status = module_install.update(tool)
         if not exit_status and all:
@@ -497,10 +502,10 @@ def create_module(ctx, tool, dir, author, label, meta, no_meta, force, conda_nam
     """
     Create a new DSL2 module from the nf-core template.
 
-    If <directory> is a pipeline, this function creates a file called
+    If the specified directory is a pipeline, this function creates a file called
     'modules/local/tool_subtool.nf'
 
-    If <directory> is a clone of nf-core/modules, it creates or modifies files
+    If the specified directory is a clone of nf-core/modules, it creates or modifies files
     in 'modules/', 'tests/modules' and 'tests/config/pytest_modules.yml'
     """
     # Combine two bool flags into one variable

nf_core/download.py

@@ -396,6 +396,7 @@ def wf_use_local_configs(self):
             nfconfig = nfconfig_fh.read()
 
         # Replace the target string
+        log.debug(f"Replacing '{find_str}' with '{repl_str}'")
         nfconfig = nfconfig.replace(find_str, repl_str)
 
         # Append the singularity.cacheDir to the end if we need it
@@ -407,6 +408,7 @@ def wf_use_local_configs(self):
             )
 
         # Write the file out again
+        log.debug(f"Updating '{nfconfig_fn}'")
         with open(nfconfig_fn, "w") as nfconfig_fh:
             nfconfig_fh.write(nfconfig)
 

nf_core/launch.py

@@ -209,7 +209,7 @@ def get_pipeline_schema(self):
                     return False
 
                 self.pipeline_revision = nf_core.utils.prompt_pipeline_release_branch(wf_releases, wf_branches)
-                self.nextflow_cmd += " -r {}".format(self.pipeline_revision)
+            self.nextflow_cmd += " -r {}".format(self.pipeline_revision)
 
         # Get schema from name, load it and lint it
         try:

nf_core/lint/files_exist.py

@@ -23,9 +23,9 @@ def files_exist(self):
         .markdownlint.yml
         .github/.dockstore.yml
         .github/CONTRIBUTING.md
-        .github/ISSUE_TEMPLATE/bug_report.md
+        .github/ISSUE_TEMPLATE/bug_report.yml
         .github/ISSUE_TEMPLATE/config.yml
-        .github/ISSUE_TEMPLATE/feature_request.md
+        .github/ISSUE_TEMPLATE/feature_request.yml
         .github/PULL_REQUEST_TEMPLATE.md
         .github/workflows/branch.yml
         .github/workflows/ci.yml
@@ -36,7 +36,6 @@ def files_exist(self):
         assets/email_template.txt
         assets/nf-core-PIPELINE_logo.png
         assets/sendmail_template.txt
-        bin/scrape_software_versions.py
         conf/modules.config
         conf/test.config
         conf/test_full.config
@@ -52,7 +51,6 @@ def files_exist(self):
         lib/NfcoreTemplate.groovy
         lib/Utils.groovy
         lib/WorkflowMain.groovy
-        modules/local/get_software_versions.nf
         nextflow_schema.json
         nextflow.config
         README.md
@@ -78,6 +76,7 @@ def files_exist(self):
         bin/markdown_to_html.r
         conf/aws.config
         .github/workflows/push_dockerhub.yml
+        .github/ISSUE_TEMPLATE/bug_report.md
 
     Files that *should not* be present:
 
@@ -109,9 +108,9 @@ def files_exist(self):
         ["README.md"],
         [os.path.join(".github", ".dockstore.yml")],
         [os.path.join(".github", "CONTRIBUTING.md")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "bug_report.md")],
+        [os.path.join(".github", "ISSUE_TEMPLATE", "bug_report.yml")],
         [os.path.join(".github", "ISSUE_TEMPLATE", "config.yml")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.md")],
+        [os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.yml")],
         [os.path.join(".github", "PULL_REQUEST_TEMPLATE.md")],
         [os.path.join(".github", "workflows", "branch.yml")],
         [os.path.join(".github", "workflows", "ci.yml")],
@@ -121,7 +120,6 @@ def files_exist(self):
         [os.path.join("assets", "email_template.txt")],
         [os.path.join("assets", "sendmail_template.txt")],
         [os.path.join("assets", f"nf-core-{short_name}_logo.png")],
-        [os.path.join("bin", "scrape_software_versions.py")],
         [os.path.join("conf", "modules.config")],
         [os.path.join("conf", "test.config")],
         [os.path.join("conf", "test_full.config")],
@@ -135,7 +133,6 @@ def files_exist(self):
         [os.path.join("lib", "NfcoreTemplate.groovy")],
         [os.path.join("lib", "Utils.groovy")],
         [os.path.join("lib", "WorkflowMain.groovy")],
-        [os.path.join("modules", "local", "get_software_versions.nf")],
     ]
 
     files_warn = [
@@ -156,6 +153,8 @@ def files_exist(self):
         os.path.join("bin", "markdown_to_html.r"),
         os.path.join("conf", "aws.config"),
         os.path.join(".github", "workflows", "push_dockerhub.yml"),
+        os.path.join(".github", "ISSUE_TEMPLATE", "bug_report.md"),
+        os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.md"),
     ]
     files_warn_ifexists = [".travis.yml"]