Merge pull request #9 from Sage-Bionetworks-Workflows/dev

[IBCDPE-589] Catch up `main` with `dev`

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# sage/dcqc: Contributing Guidelines
+# sage-bionetworks-workflows/nf-dcqc: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving sage/dcqc.
+Many thanks for taking an interest in improving sage-bionetworks-workflows/nf-dcqc.
 
-We try to manage the required tasks for sage/dcqc using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for sage-bionetworks-workflows/nf-dcqc using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for sage/dcqc, the standard workflow is as follows:
+If you'd like to write some code for sage-bionetworks-workflows/nf-dcqc, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [sage/dcqc issues](https://github.com/sage/dcqc/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [sage/dcqc repository](https://github.com/sage/dcqc) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [sage-bionetworks-workflows/nf-dcqc issues](https://github.com/sage-bionetworks-workflows/nf-dcqc/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [sage-bionetworks-workflows/nf-dcqc repository](https://github.com/sage-bionetworks-workflows/nf-dcqc) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -52,7 +52,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the sage/dcqc code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the sage-bionetworks-workflows/nf-dcqc code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -102,7 +102,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/sage/dcqc/codespaces)
+- Open the repo in [Codespaces](https://github.com/sage-bionetworks-workflows/nf-dcqc/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,52 +2,52 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- 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 you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* Nextflow version _(eg. 22.10.1)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of sage/dcqc _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - 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 you used
+        to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: "$ nextflow run ...
+
+
+        Some output where something broke
+
+        "
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: "* Nextflow version _(eg. 22.10.1)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of sage-bionetworks-workflows/nf-dcqc _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the sage/dcqc pipeline
+description: Suggest an idea for the sage-bionetworks-workflows/nf-dcqc pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# sage/dcqc pull request
+# sage-bionetworks-workflows/nf-dcqc pull request
 
-Many thanks for contributing to sage/dcqc!
+Many thanks for contributing to sage-bionetworks-workflows/nf-dcqc!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/sage/dcqc/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/sage-bionetworks-workflows/nf-dcqc/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sage/dcqc/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sage-bionetworks-workflows/nf-dcqc/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'sage/dcqc'
+        if: github.repository == 'sage-bionetworks-workflows/nf-dcqc'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == sage/dcqc ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == sage-bionetworks-workflows/nf-dcqc ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # 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

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "22.10.4"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
@@ -36,8 +36,8 @@ jobs:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+        env:
+          SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
         run: |
+          nextflow secrets set SYNAPSE_AUTH_TOKEN "${SYNAPSE_AUTH_TOKEN}"
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

.nf-core.yml

@@ -1,15 +1,15 @@
 repository_type: pipeline
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-dcqc_logo_light.png
-  - docs/images/nf-core-dcqc_logo_light.png
-  - docs/images/nf-core-dcqc_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-dcqc_logo_light.png
+    - docs/images/nf-core-dcqc_logo_light.png
+    - docs/images/nf-core-dcqc_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
+    - manifest.name
+    - manifest.homePage
   multiqc_config:
-  - report_comment
+    - report_comment

README.md

@@ -1,6 +1,6 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.4-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -27,7 +27,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.4`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 
@@ -52,6 +52,16 @@ On release, automated continuous integration tests run the pipeline on a full-si
    nextflow run sage/dcqc --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
+## Special Considerations for Running `nf-dcqc` on Nextflow Tower
+
+`nf-dcqc` leverages the reports feature when executed on Tower. This is done by pointing Tower to the generated `output.csv` file which is saved to `params.outdir` after a successful run. By default, the `outdir` for the workflow is set to a local directory called `results`. This does not work on Nextflow Tower runs, as you will not have access to the `results` directory once the job has completed. Thus, the `outdir` should be set to an S3 bucket location that the Tower workspace you are using has access to. For example, in the `pipeline parameters` for a Tower run, you can provide YAML such as:
+
+```yaml
+outdir: s3://example-project-tower-bucket/dcqc_output
+```
+
+From the reports tab within your workflow run, you can view and download the generated `output.csv` file.
+
 ## Credits
 
 sage/dcqc was originally written by Bruno Grande <bruno.grande@sagebionetworks.org>.

assets/email_template.html

@@ -4,21 +4,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="sage/dcqc: Nextflow Workflow for Data Coordination Quality Control">
-  <title>sage/dcqc Pipeline Report</title>
+  <meta name="description" content="sage-bionetworks-workflows/nf-dcqc: Nextflow Workflow for Data Coordination Quality Control">
+  <title>sage-bionetworks-workflows/nf-dcqc Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>sage/dcqc v${version}</h1>
+<h1>sage-bionetworks-workflows/nf-dcqc v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">sage/dcqc execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">sage-bionetworks-workflows/nf-dcqc execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -27,7 +27,7 @@ <h4 style="margin-top:0; color: inherit;">sage/dcqc execution completed unsucces
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        sage/dcqc execution completed successfully!
+        sage-bionetworks-workflows/nf-dcqc execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>sage/dcqc</p>
-<p><a href="https://github.com/sage/dcqc">https://github.com/sage/dcqc</a></p>
+<p>sage-bionetworks-workflows/nf-dcqc</p>
+<p><a href="https://github.com/sage-bionetworks-workflows/nf-dcqc">https://github.com/sage-bionetworks-workflows/nf-dcqc</a></p>
 
 </div>
 

assets/email_template.txt

@@ -1,10 +1,10 @@
 Run Name: $runName
 
 <% if (success){
-    out << "## sage/dcqc execution completed successfully! ##"
+    out << "## sage-bionetworks-workflows/nf-dcqc execution completed successfully! ##"
 } else {
     out << """####################################################
-## sage/dcqc execution completed unsuccessfully! ##
+## sage-bionetworks-workflows/nf-dcqc execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -27,5 +27,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-sage/dcqc
-https://github.com/sage/dcqc
+sage-bionetworks-workflows/nf-dcqc
+https://github.com/sage-bionetworks-workflows/nf-dcqc

assets/sendmail_template.txt

@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="sage-dcqc_logo.png"
+Content-Type: image/png;name="sage-bionetworks-workflows-nf-dcqc_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="sage-dcqc_logo_light.png"
+Content-Disposition: inline; filename="sage-bionetworks-workflows-nf-dcqc_logo_light.png"
 
-<% out << new File("$projectDir/assets/sage-dcqc_logo_light.png").
+<% out << new File("$projectDir/assets/sage-bionetworks-workflows-nf-dcqc_logo_light.png").
     bytes.
     encodeBase64().
     toString().

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -24,7 +23,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }
@@ -59,6 +57,12 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withLabel:dcqc {
+        container   = 'ghcr.io/sage-bionetworks-workflows/py-dcqc:latest'
+        secret      = [
+            'SYNAPSE_AUTH_TOKEN'
+        ]
+    }
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }