Merge branch 'dev' into feature/fcssummary

.github/CONTRIBUTING.md

@@ -52,9 +52,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :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`.
+- On your own fork, make a new branch `patch` based on `upstream/main`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- A PR should be made on `main` from patch to directly this particular bug.
 
 ## Pipeline contribution conventions
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ 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/plant-food-research-open/assemblyqc/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/plant-food-research-open/assemblyqc/tree/main/.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/plant-food-research-open/assemblyqc/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/plant-food-research-open/assemblyqc/tree/main/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/branch.yml

@@ -1,15 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'plant-food-research-open/assemblyqc'
         run: |
@@ -22,7 +22,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +32,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{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.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{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.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,10 +17,10 @@ on:
       - edited
       - synchronize
     branches:
-      - master
+      - main
   pull_request_target:
     branches:
-      - master
+      - main
 
 env:
   NXF_ANSI_LOG: false

.github/workflows/linting.yml

@@ -62,6 +62,7 @@ jobs:
             --key files_unchanged \
             --key merge_markers \
             --key modules_config \
+            --key multiqc_config \
             --key nextflow_config \
             --key nfcore_yml \
             --key pipeline_name_conventions \

.nf-core.yml

@@ -10,18 +10,18 @@ lint:
     - assets/multiqc_config.yml
     - conf/igenomes.config
   files_unchanged:
-    - CODE_OF_CONDUCT.md
-    - assets/nf-core-assemblyqc_logo_light.png
-    - docs/images/nf-core-assemblyqc_logo_light.png
-    - docs/images/nf-core-assemblyqc_logo_dark.png
     - docs/README.md
+    - .github/PULL_REQUEST_TEMPLATE.md
     - .github/CONTRIBUTING.md
     - .github/workflows/linting.yml
+    - .github/workflows/branch.yml
     - LICENSE
   nextflow_config:
     - manifest.name
     - manifest.homePage
+  multiqc_config: False
   template_strings: False
+  multiqc_config: False
 nf_core_version: 2.14.1
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -8,11 +8,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 1. Created summary presence/absence tables for NCBI FCS modules [#88](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/88)
+2. Added min. system requirements [#91](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/91)
 
 ### `Fixed`
 
 1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95)
 2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false
+3. Changed default branch name from `master` to `main` in nf-core template files
 
 ### `Dependencies`
 

assets/schema_input.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/assets/schema_input.json",
     "title": "plant-food-research-open/assemblyqc pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",

assets/schema_xref_assemblies.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/assets/schema_xref_assemblies.json",
+    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/assets/schema_xref_assemblies.json",
     "title": "plant-food-research-open/assemblyqc pipeline - params.synteny_xref_assemblies schema",
     "description": "Schema for the file provided with params.synteny_xref_assemblies",
     "type": "array",

docs/usage.md

@@ -1,4 +1,34 @@
-# plant-food-research-open/assemblyqc: Usage
+# plant-food-research-open/assemblyqc: Usage<!-- omit in toc -->
+
+- [Assemblysheet input](#assemblysheet-input)
+- [External databases](#external-databases)
+  - [NCBI FCS GX database](#ncbi-fcs-gx-database)
+  - [Kraken2](#kraken2)
+  - [BUSCO](#busco)
+- [Other parameters](#other-parameters)
+  - [Assemblathon stats](#assemblathon-stats)
+  - [NCBI FCS GX](#ncbi-fcs-gx)
+  - [BUSCO](#busco-1)
+  - [TIDK](#tidk)
+  - [HiC](#hic)
+  - [Synteny analysis](#synteny-analysis)
+  - [Merqury K-mer analysis](#merqury-k-mer-analysis)
+- [Minimum System Requirements](#minimum-system-requirements)
+- [Running the pipeline](#running-the-pipeline)
+  - [Updating the pipeline](#updating-the-pipeline)
+  - [Reproducibility](#reproducibility)
+- [Core Nextflow arguments](#core-nextflow-arguments)
+  - [`-profile`](#-profile)
+  - [`-resume`](#-resume)
+  - [`-c`](#-c)
+- [Custom configuration](#custom-configuration)
+  - [Resource requests](#resource-requests)
+  - [Custom Containers](#custom-containers)
+  - [Custom Tool Arguments](#custom-tool-arguments)
+  - [nf-core/configs](#nf-coreconfigs)
+- [Azure Resource Requests](#azure-resource-requests)
+- [Running in the background](#running-in-the-background)
+- [Nextflow memory requirements](#nextflow-memory-requirements)
 
 ## Assemblysheet input
 
@@ -95,6 +125,13 @@ See following assemblysheet examples for MERQURY analysis.
 
 The data for these examples comes from: [umd.edu](https://obj.umiacs.umd.edu/marbl_publications/triobinning/index.html)
 
+## Minimum System Requirements
+
+All the modules have been tested to work on a single machine with 10 CPUs + 30 GBs of memory, except NCBI FCS GX and Kraken2. Their minimum requirements are:
+
+- NCBI FCS GX: 1 CPU + 512 GBs memory
+- Kraken2: 1 CPU + 200 GBs memory
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:

nextflow_schema.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json",
     "title": "plant-food-research-open/assemblyqc pipeline parameters",
     "description": "A NextFlow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.",
     "type": "object",