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3476908
Dev version bump to 2.3.0dev
jfy133 Oct 21, 2020
f2a326d
Merge pull request #588 from nf-core/master
jfy133 Oct 22, 2020
1827383
Template update for nf-core/tools version 1.11
nf-core-bot Oct 27, 2020
38d2b38
Merge branch 'dev' into TEMPLATE
jfy133 Oct 27, 2020
a0fe453
Linting
jfy133 Oct 27, 2020
f5f62af
Linting
jfy133 Oct 27, 2020
21a4400
Merge pull request #595 from nf-core/TEMPLATE
apeltzer Oct 28, 2020
ff7b8f6
Apparently we are big fans of Irina...
jfy133 Oct 30, 2020
22f90a9
Update usage.md
TCLamnidis Oct 30, 2020
a99ce04
Merge pull request #599 from nf-core/TCLamnidis-patch-1
TCLamnidis Oct 30, 2020
561e2a3
fix aws full test profiles
ggabernet Nov 1, 2020
dcae01e
remove awsfulltest config
ggabernet Nov 1, 2020
8b41ab8
Merge pull request #600 from ggabernet/dev
apeltzer Nov 2, 2020
81d96be
Add stress-test profile
jfy133 Nov 3, 2020
fb5d671
fix param typo
jfy133 Nov 4, 2020
e13f80b
Reset 2.2.1 back up to dev
jfy133 Nov 4, 2020
c073895
Update CHANGELOG.md
jfy133 Nov 4, 2020
e8e693e
Push back up to 2.3
jfy133 Nov 4, 2020
9be472b
Bump back up to 2.3.0dev
jfy133 Nov 4, 2020
31f9e0e
Update nextflow.config
jfy133 Nov 4, 2020
4051c61
Remove Irina duplicate
jfy133 Nov 4, 2020
916ae4b
Merge branch 'dev' into master-to-dev
jfy133 Nov 4, 2020
e0f2a88
Typo
jfy133 Nov 4, 2020
a6348fc
Merge pull request #603 from nf-core/master-to-dev
jfy133 Nov 4, 2020
9c1d7e4
Update test_stresstest_human.config
apeltzer Nov 5, 2020
b3d742c
Really long walltimes!
jfy133 Nov 6, 2020
60b11ff
Reimplement AdapterRemovalFixPrefix so DeDup can work properly when s…
jfy133 Nov 6, 2020
2232c2c
Update test_stresstest_human.config
jfy133 Nov 9, 2020
a706788
Fixredirectg for FixPrefix commands
jfy133 Nov 9, 2020
80f263f
Merge pull request #604 from nf-core/adapterremoval-prefix-fix
jfy133 Nov 9, 2020
a6c0100
Try reducing memory requirements and always errorStrategy on retry
jfy133 Nov 12, 2020
ede77f7
Add eager2 metromap
jfy133 Nov 12, 2020
ad86ab2
Merge pull request #606 from nf-core/jfy133-patch-1
jfy133 Nov 12, 2020
25a70d6
Remove GATK manual Jar specification and drop version for next patch
jfy133 Nov 13, 2020
91721d3
Remove leftover run:
jfy133 Nov 13, 2020
eea2dd0
Actually remove use of the jars :facepalm:
jfy133 Nov 13, 2020
2666385
Update usage.md
jfy133 Nov 13, 2020
dbca8ea
Update nextflow_schema.json
jfy133 Nov 13, 2020
85c853a
Clarified merging details in TSV input section
scarlhoff Nov 13, 2020
1d7162e
Update test_stresstest_human.config
jfy133 Nov 16, 2020
d67d0dc
Update nextflow_schema.json
jfy133 Nov 16, 2020
5105f16
Merge pull request #611 from scarlhoff/dev
jfy133 Nov 16, 2020
6d6cef3
Update README.md
jfy133 Nov 16, 2020
9217a24
Fix link for Selina
jfy133 Nov 16, 2020
b767519
Fix circularmapper error reported in https://github.com/nf-core/eager…
jfy133 Nov 16, 2020
d5aff01
Merge pull request #613 from nf-core/circular-mapper-fix
apeltzer Nov 16, 2020
13687a5
Merge branch 'dev' into gatk3
jfy133 Nov 16, 2020
f3c8be4
Fix GHA fails due to deprecated variables
jfy133 Nov 17, 2020
cf20fcb
Merge branch 'gatk3' of github.com:nf-core/eager into gatk3
jfy133 Nov 17, 2020
23be10d
Merge pull request #609 from nf-core/gatk3
apeltzer Nov 17, 2020
9e1f30b
Template update for nf-core/tools version 1.12
jfy133 Nov 30, 2020
e630cd9
Manual Template merge to tools 1.12
jfy133 Nov 30, 2020
5f60d08
Linting fixes
jfy133 Nov 30, 2020
7992d07
Update CHANGELOG.md
jfy133 Nov 30, 2020
4680f3e
Moar linting
jfy133 Nov 30, 2020
aa83851
Bump retries
jfy133 Dec 1, 2020
0ff78c5
Merge pull request #2 from nf-core/dev
jfy133 Dec 2, 2020
37f5930
Release version bump
jfy133 Dec 2, 2020
0d7131f
Merge pull request #620 from jfy133/dev
jfy133 Dec 2, 2020
1937534
Template update for nf-core/tools version 1.12.1
nf-core-bot Dec 3, 2020
0350331
Update test_stresstest_human.config
jfy133 Dec 4, 2020
03925e7
Merge pull request #3 from nf-core/dev
jfy133 Dec 7, 2020
0fa9c7a
Merged changes from nf-core template
jfy133 Dec 7, 2020
21e6e8c
Fix typos repoted by @ashildv
jfy133 Dec 7, 2020
c78bc37
Merge pull request #625 from jfy133/merging-template-updates
jfy133 Dec 7, 2020
e0c830c
Apply suggestions from code review
jfy133 Dec 8, 2020
d85662a
Remove pipeline options in lieu of nextflow_schema.json
jfy133 Dec 8, 2020
c971f1e
Remove ToC
jfy133 Dec 8, 2020
40fbd1e
Add metro map
jfy133 Dec 8, 2020
10dd47e
Changes from review
jfy133 Dec 8, 2020
e2f7109
linting fixes
jfy133 Dec 8, 2020
0a71786
fix some heading levels
jfy133 Dec 8, 2020
55f399a
Fix link in schema
jfy133 Dec 8, 2020
5ead4b0
Update release date
jfy133 Dec 9, 2020
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119 changes: 61 additions & 58 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@ If you'd like to write some code for nf-core/eager, the standard workflow is as
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 [code contribution guidelines](https://github.com/nf-core/eager/blob/dev/.github/CONTRIBUTING.md))
4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires nf-core tools >= 1.10).
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

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/).
Expand All @@ -31,14 +31,14 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t

There are typically two types of tests that run:

### Lint Tests
### Lint tests

`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.

If any failures or warnings are encountered, please follow the listed URL for more documentation.

### Pipeline Tests
### Pipeline tests

Each `nf-core` pipeline should be set up with a minimal set of test-data.
`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
Expand All @@ -55,38 +55,82 @@ These tests are run both with the latest available version of `Nextflow` and als

## Getting help

For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/eager/latest/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/eager/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).

# Code Contribution Guidelines
## Pipeline contribution conventions

To make the EAGER2 code and processing logic more understandable for new contributors, and to ensure quality. We are making an attempt to somewhat-standardise the way the code is written.
To make the nf-core/eager 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.

If you wish to contribute a new module, please use the following coding standards.
### Adding a new step

The typical workflow for adding a new module is as follows:
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 (or re-routing block, see below).
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 .`)
5. Add any new flags/options to `nextflow_schema.json` **with help text** (with `nf-core schema build .`)
6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
7. Add sanity checks for all relevant parameters.
8. 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`.
9. Do local tests that the new code works properly and as expected.
10. Add a new test command in `.github/workflow/ci.yaml`.
11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
12. 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.
13. Add new flags/options to 'usage' documentation under `docs/usage.md`.
14. Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.

## Default Values
### Default values

Default values should go in `nextflow.config` under the `params` scope, and `nextflow_schema.json` (latter with `nf-core schema build .`)
Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

## Default resource processes
Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.

Defining recommended 'minimum' resource requirements (CPUs/Memory) for a process should be defined in `conf/base.config`. This can be utilised within the process using `${task.cpu}` or `${task.memory}` variables in the `script:` block.
### 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/%7B%7Bcookiecutter.name_noslash%7D%7D/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)

### 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

Expand Down Expand Up @@ -164,44 +208,3 @@ if (params.run_fastp) {
}

```

## Naming Schemes

Please use the following naming schemes, to make it easy to understand what is going where.

* process output: `ch_output_from_<process>`(this should always go into the bypass statement described above).
* skipped process output: `ch_<previousstage>_for_<skipprocess>`(this goes out of the bypass statement described above)
* process inputs: `ch_<previousstage>_for_<process>` (this goes into a process)

## Nextflow Version Bumping

If you have agreement from reviewers, you may bump the 'default' minimum version of nextflow (e.g. for testing), with `nf-core bump-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 tools --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 block entry to the `OrderedDict` for formatting in MultiQC.

> If a tool does not unfortunately offer any printing of version data, you may add this 'manually' e.g. with `echo "v1.1" > v_<YOUR_TOOL>.txt`

## Images and Figures

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).

For the overview image we follow the nf-core [style guidelines](https://nf-co.re/developers/design_guidelines).
43 changes: 23 additions & 20 deletions .github/ISSUE_TEMPLATE/bug_report.md
Original file line number Diff line number Diff line change
@@ -1,28 +1,29 @@
# nf-core/eager bug report
---
name: Bug report
about: Report something that is broken or incorrect
labels: bug
---

<!--
# nf-core/eager bug report

Hi there!

Thanks for telling us about a problem with the pipeline.

Please delete this text and anything that's not relevant from the template below:
-->

## Check Documentation

Have you checked in the following places for your error?:

- [ ] [Frequently Asked Questions](https://github.com/nf-core/eager/blob/master/docs/usage.md#troubleshooting-and-faqs)
(for nf-core/eager specific information)
- [ ] [Troubleshooting](https://nf-co.re/usage/troubleshooting)
(for nf-core specific information)
I have checked the following places for your error:

Please also check the the corresponding version's documentation on github, if not
testing the latest release.
- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [ ] [nf-core/eager pipeline documentation](https://nf-co.re/nf-core/eager/usage)
- nf-core/eager FAQ/troubleshooting can be found [here](https://nf-co.re/eager/usage#troubleshooting-and-faqs)

## Describe the bug
## Description of the bug

A clear and concise description of what the bug is.
<!-- A clear and concise description of what the bug is. -->

## Steps to reproduce

Expand All @@ -33,13 +34,15 @@ Steps to reproduce the behaviour:

## Expected behaviour

A clear and concise description of what you expected to happen.
<!-- A clear and concise description of what you expected to happen. -->

## Log files

1. The command used to run the pipeline
2. The `.nextflow.log` file (which is a hidden file in whichever place you _ran_
the pipeline from - not necessarily in the output directory!)
Have you provided the following extra information/files:

- [ ] The command used to run the pipeline
- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the pipeline -->
- [ ] The exact error: <!-- [Please provide your error message] -->

## System

Expand All @@ -54,10 +57,10 @@ A clear and concise description of what you expected to happen.

## Container engine

- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
- version: <!-- [e.g. 2.1.0] -->
- Image tag: <!-- [e.g. nfcore/eager:2.1.0] -->
- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
- version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/eager:1.0.0] -->

## Additional context

Add any other context about the problem here.
<!-- Add any other context about the problem here. -->
8 changes: 8 additions & 0 deletions .github/ISSUE_TEMPLATE/config.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
blank_issues_enabled: false
contact_links:
- name: Join nf-core
url: https://nf-co.re/join
about: Please join the nf-core community here
- name: "Slack #eager channel"
url: https://nfcore.slack.com/channels/eager
about: Discussion about the nf-core/eager pipeline
8 changes: 7 additions & 1 deletion .github/ISSUE_TEMPLATE/feature_request.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# nf-core/eager feature request
---
name: Feature request
about: Suggest an idea for the nf-core website
labels: enhancement
---

<!--
# nf-core/eager feature request

Hi there!

Expand Down
25 changes: 15 additions & 10 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
@@ -1,21 +1,26 @@
# nf-core/eager pull request
<!--
# nf-core/eager pull request

Many thanks for contributing to nf-core/eager!

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/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
-->

## PR checklist

- [ ] This comment contains a description of changes (with reason)
- [ ] 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 necessary, also make a PR on the [nf-core/eager branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/eager)
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --paired_end`).
- [ ] Make sure your code lints ([`nf-core lint .`](https://nf-co.re/tools)).
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated

**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
- [ ] 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`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and authors/contributors).
4 changes: 2 additions & 2 deletions .github/markdownlint.yml
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
# Markdownlint configuration file
default: true,
default: true
line-length: false
no-duplicate-header:
siblings_only: true
no-inline-html:
no-inline-html:
allowed_elements:
- img
- p
Expand Down
9 changes: 5 additions & 4 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,9 @@ name: nf-core AWS full size tests
# It runs the -profile 'test_full' on AWS batch

on:
release:
types: [published]
workflow_run:
workflows: ["nf-core Docker push (release)"]
types: [completed]
workflow_dispatch:

jobs:
Expand All @@ -15,7 +16,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Setup Miniconda
uses: goanpeca/setup-miniconda@v1.0.2
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.7
Expand All @@ -38,4 +39,4 @@ jobs:
--job-name nf-core-eager \
--job-queue $AWS_JOB_QUEUE \
--job-definition $AWS_JOB_DEFINITION \
--container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile awsfulltest --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
--container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
2 changes: 1 addition & 1 deletion .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Setup Miniconda
uses: goanpeca/setup-miniconda@v1.0.2
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.7
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ 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`
on:
pull_request:
pull_request_target:
branches: [master]

jobs:
Expand Down
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