Wipe everything and start from scratch

.editorconfig

@@ -0,0 +1,24 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js,cff}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+
+[/assets/email*]
+indent_size = unset

.gitattributes

@@ -1 +1,3 @@
 *.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -15,11 +15,10 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for nf-core/eager, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/eager issues](https://github.com/nf-core/eager/issues) to avoid duplicating work
-    * If there isn't one already, please create one so that others know you're working on this
+1. Check that there isn't already an issue about your idea in the [nf-core/eager issues](https://github.com/nf-core/eager/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 [nf-core/eager repository](https://github.com/nf-core/eager) 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).
+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
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -49,9 +48,9 @@ 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`.
-* Fix the bug, and bump version (X.Y.Z+1).
-* A PR should be made on `master` from patch to directly this particular bug.
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
@@ -68,142 +67,37 @@ If you wish to contribute a new step, please use the following coding standards:
 1. Define the corresponding input channel into your new process from the expected previous process channel
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
-4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
-6. Add sanity checks for all relevant parameters.
-7. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
-8. Do local tests that the new code works properly and as expected.
-9. Add a new test command in `.github/workflow/ci.yaml`.
-10. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-11. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-12. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+4. Add any new parameters to `nextflow.config` with a default (see below).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+6. Add sanity checks and validation for all relevant parameters.
+7. Perform local tests to validate that the new code works as expected.
+8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
+Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-:warning: Note that in nf-core/eager we currently have our own custom process labels, so please check `base.config`!
-
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-* initial process channel: `ch_output_from_<process>`
-* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
-* skipped process output: `ch_<previousstage>_for_<skipprocess>`(this goes out of the bypass statement described above)
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 
 If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
 
-### Software version reporting
-
-If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
-
-Add to the script block of the process, something like the following:
-
-```bash
-<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-or
-
-```bash
-<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-You then need to edit the script `bin/scrape_software_versions.py` to:
-
-1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
-2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
-
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
-
-For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License. It can be found for download here [here](https://fonts.google.com/specimen/Kalam).
-
-## Process Concept
-
-We are providing a highly configurable pipeline, with many options to turn on and off different processes in different combinations. This can make a very complex graph structure that can cause a large amount of duplicated channels coming out of every process to account for each possible combination.
-
-The EAGER pipeline can currently be broken down into the following 'stages', where a stage is a collection of  non-terminal mutually exclusive processes, which is the output of which is used for another file reporting module (but not reporting!) .
-
-* Input
-* Convert BAM
-* PolyG Clipping
-* AdapterRemoval
-* Mapping (either `bwa`, `bwamem`, or `circularmapper`)
-* BAM Filtering
-* Deduplication (either `dedup` or `markduplicates`)
-* BAM Trimming
-* PMDtools
-* Genotyping
-
-Every step can potentially be skipped, therefore the output of a previous stage must be able to be passed to the next stage, if the given stage is not run.
-
-To somewhat simplify this logic, we have implemented the following structure.
-
-The concept is as follows:
-
-* Every 'stage' of the pipeline (i.e. collection of mutually exclusive processes) must always have a if else statement following it.
-* This if else 'bypass' statement collects and standardises all possible input files into single channel(s) for the next stage.
-* Importantly - within the bypass statement, a channel from the previous stage's bypass mixes into these output channels. This additional channel is named `ch_previousstage_for_skipcurrentstage`. This contains the output from the previous stage, i.e. not the modified version from the current stage.
-* The bypass statement works as follows:
-  * If the current stage is turned on: will mix the previous stage and current stage output and filter for file suffixes unique to the current stage output
-  * If the current stage is turned off or skipped: will mix the previous stage and current stage output. However as there there is no files in the output channel from the current stage, no filtering is required and the files in the 'ch_XXX_for_skipXXX' stage will be used.
-
- This ensures the same channel inputs to the next stage is 'homogeneous' - i.e. all comes from the same source (the bypass statement)
-
- An example schematic can be given as follows
-
-```nextflow
- // PREVIOUS STAGE OUTPUT
-if (params.run_bam_filtering) {
-    ch_input_for_skipconvertbam.mix(ch_output_ch_convertbam)
-        .filter{ it =~/.*converted.fq/}
-        .into { ch_convertbam_for_fastp; ch_convertbam_for_skipfastp }
-} else {
-    ch_input_for_skipconvertbam
-        .into { ch_convertbam_for_fastp; ch_convertbam_for_skipfastp }
-}
-
-// SKIPPABLE CURRENT STAGE PROCESS
-process fastp {
-    publishDir "${params.outdir}/fastp", mode: 'copy'
-
-    when:
-    params.run_fastp
-
-    input:
-    file fq from ch_convertbam_for_fastp
-
-    output:
-    file "*pG.fq" into ch_output_from_fastp
-
-    script:
-    """
-    echo "I have been fastp'd" > ${fq}  
-    mv ${fq} ${fq}.pG.fq
-    """
-}
-
-// NEXT STAGE INPUT PREPARATION
-if (params.run_fastp) {
-    ch_convertbam_for_skipfastp.mix(ch_output_from_fastp)
-        .filter { it =~/.*pG.fq/ }
-        .into { ch_fastp_for_adapterremoval; ch_fastp_for_skipadapterremoval }
-} else {
-    ch_convertbam_for_skipfastp
-        .into { ch_fastp_for_adapterremoval; ch_fastp_for_skipadapterremoval }
-}
-
- ```

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,50 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/eager pipeline documentation](https://nf-co.re/eager/usage)
+
+  - 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. 21.10.3)_
+        * 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 nf-core/eager _(eg. 1.1, 1.5, 1.8.2)_

.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 the nf-core/eager pipeline
+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/PULL_REQUEST_TEMPLATE.md

@@ -10,17 +10,14 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
 -->
-<!-- markdownlint-disable ul-indent -->
 
 ## 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 - add to the software_versions process and a regex to `scrape_software_versions.py`
-    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](<https://github.com/>nf-core/eager/tree/master/.github/CONTRIBUTING.md)
-    - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint .`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] 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.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.