From 8159e1010e10949958733339bcef94141455c555 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 16 May 2022 10:16:03 +0000
Subject: [PATCH] Template update for nf-core/tools version 2.4
---
.github/workflows/awsfulltest.yml | 3 -
.github/workflows/awstest.yml | 3 -
.github/workflows/branch.yml | 3 +-
.github/workflows/ci.yml | 2 -
.github/workflows/fix-linting.yml | 55 ++++++++++
.github/workflows/linting.yml | 4 +-
.github/workflows/linting_comment.yml | 1 -
.prettierignore | 9 ++
CHANGELOG.md | 2 +-
README.md | 25 ++---
assets/email_template.html | 142 ++++++++------------------
bin/check_samplesheet.py | 16 ++-
nextflow.config | 4 +-
13 files changed, 137 insertions(+), 132 deletions(-)
create mode 100644 .github/workflows/fix-linting.yml
create mode 100644 .prettierignore
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 4d71d9a..82c1a4e 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -28,6 +28,3 @@ jobs:
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
- nextflow_config: |
- process.errorStrategy = 'retry'
- process.maxRetries = 3
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index f892cfd..5cd0714 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -23,6 +23,3 @@ jobs:
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/hic/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
- nextflow_config: |
- process.errorStrategy = 'retry'
- process.maxRetries = 3
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 3636672..b92e3d2 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/hic'
run: |
- "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+ { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/hic ]] && [[ $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
@@ -42,4 +42,3 @@ jobs:
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false
-#
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4940ecf..738e174 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -48,5 +48,3 @@ jobs:
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-#
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
new file mode 100644
index 0000000..502eff9
--- /dev/null
+++ b/.github/workflows/fix-linting.yml
@@ -0,0 +1,55 @@
+name: Fix linting from a comment
+on:
+ issue_comment:
+ types: [created]
+
+jobs:
+ deploy:
+ # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+ if: >
+ contains(github.event.comment.html_url, '/pull/') &&
+ contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+ github.repository == 'nf-core/hic'
+ runs-on: ubuntu-latest
+ steps:
+ # Use the @nf-core-bot token to check out so we can push later
+ - uses: actions/checkout@v3
+ with:
+ token: ${{ secrets.nf_core_bot_auth_token }}
+
+ # Action runs on the issue comment, so we don't get the PR by default
+ # Use the gh cli to check out the PR
+ - name: Checkout Pull Request
+ run: gh pr checkout ${{ github.event.issue.number }}
+ env:
+ GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+ - uses: actions/setup-node@v2
+
+ - name: Install Prettier
+ run: npm install -g prettier @prettier/plugin-php
+
+ # Check that we actually need to fix something
+ - name: Run 'prettier --check'
+ id: prettier_status
+ run: |
+ if prettier --check ${GITHUB_WORKSPACE}; then
+ echo "::set-output name=result::pass"
+ else
+ echo "::set-output name=result::fail"
+ fi
+
+ - name: Run 'prettier --write'
+ if: steps.prettier_status.outputs.result == 'fail'
+ run: prettier --write ${GITHUB_WORKSPACE}
+
+ - name: Commit & push changes
+ if: steps.prettier_status.outputs.result == 'fail'
+ run: |
+ git config user.email "core@nf-co.re"
+ git config user.name "nf-core-bot"
+ git config push.default upstream
+ git add .
+ git status
+ git commit -m "[automated] Fix linting with Prettier"
+ git push
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index e9cf5de..77358de 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -48,7 +48,7 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v3
with:
python-version: "3.6"
architecture: "x64"
@@ -78,5 +78,3 @@ jobs:
lint_log.txt
lint_results.md
PR_number.txt
-
-#
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 91c487a..04758f6 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -26,4 +26,3 @@ jobs:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }}
path: linting-logs/lint_results.md
-#
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..d0e7ae5
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,9 @@
+email_template.html
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 87c2402..1b0b90b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## v1.3.1 - [date]
+## v1.4.0dev - [date]
Initial release of nf-core/hic, created with the [nf-core](https://nf-co.re/) template.
diff --git a/README.md b/README.md
index eefaec9..ff1e81d 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,19 @@
-#  
+#  
[](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+CI%22)
[](https://github.com/nf-core/hic/actions?query=workflow%3A%22nf-core+linting%22)
-[](https://nf-co.re/hic/results)
-[](https://doi.org/10.5281/zenodo.XXXXXXX)
-
-[](https://www.nextflow.io/)
-[](https://docs.conda.io/en/latest/)
-[](https://www.docker.com/)
-[](https://sylabs.io/docs/)
-
-[](https://nfcore.slack.com/channels/hic)
-[](https://twitter.com/nf_core)
-[](https://www.youtube.com/c/nf-core)
+[](https://nf-co.re/hic/results)
+[](https://doi.org/10.5281/zenodo.XXXXXXX)
+
+[](https://www.nextflow.io/)
+[](https://docs.conda.io/en/latest/)
+[](https://www.docker.com/)
+[](https://sylabs.io/docs/)
+[](https://tower.nf/launch?pipeline=https://github.com/nf-core/hic)
+
+[](https://nfcore.slack.com/channels/hic)
+[](https://twitter.com/nf_core)
+[](https://www.youtube.com/c/nf-core)
## Introduction
diff --git a/assets/email_template.html b/assets/email_template.html
index 80d5dac..d207f01 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -1,111 +1,53 @@
<html>
- <head>
- <meta charset="utf-8" />
- <meta http-equiv="X-UA-Compatible" content="IE=edge" />
- <meta name="viewport" content="width=device-width, initial-scale=1" />
+<head>
+ <meta charset="utf-8">
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
- <!-- prettier-ignore -->
- <meta name="description" content="nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)" />
- <title>nf-core/hic 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" />
+ <meta name="description" content="nf-core/hic: Analysis of Chromosome Conformation Capture data (Hi-C)">
+ <title>nf-core/hic Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
- <h1>nf-core/hic v${version}</h1>
- <h2>Run Name: $runName</h2>
+<img src="cid:nfcorepipelinelogo">
- <% if (!success){ out << """
- <div
- style="
- color: #a94442;
- background-color: #f2dede;
- border-color: #ebccd1;
- padding: 15px;
- margin-bottom: 20px;
- border: 1px solid transparent;
- border-radius: 4px;
- "
- >
- <h4 style="margin-top: 0; color: inherit">nf-core/hic execution completed unsuccessfully!</h4>
+<h1>nf-core/hic v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+ out << """
+ <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+ <h4 style="margin-top:0; color: inherit;">nf-core/hic execution completed unsuccessfully!</h4>
<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
<p>The full error message was:</p>
- <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
- </div>
- """ } else { out << """
- <div
- style="
- color: #3c763d;
- background-color: #dff0d8;
- border-color: #d6e9c6;
- padding: 15px;
- margin-bottom: 20px;
- border: 1px solid transparent;
- border-radius: 4px;
- "
- >
+ <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+ </div>
+ """
+} else {
+ out << """
+ <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
nf-core/hic execution completed successfully!
- </div>
- """ } %>
+ </div>
+ """
+}
+%>
- <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
- <p>The command used to launch the workflow was as follows:</p>
- <pre
- style="
- white-space: pre-wrap;
- overflow: visible;
- background-color: #ededed;
- padding: 15px;
- border-radius: 4px;
- margin-bottom: 30px;
- "
- >
-$commandLine</pre
- >
+<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+<p>The command used to launch the workflow was as follows:</p>
+<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
- <h3>Pipeline Configuration:</h3>
- <table
- style="
- width: 100%;
- max-width: 100%;
- border-spacing: 0;
- border-collapse: collapse;
- border: 0;
- margin-bottom: 30px;
- "
- >
- <tbody style="border-bottom: 1px solid #ddd">
- <% out << summary.collect{ k,v -> "
- <tr>
- <th
- style="
- text-align: left;
- padding: 8px 0;
- line-height: 1.42857143;
- vertical-align: top;
- border-top: 1px solid #ddd;
- "
- >
- $k
- </th>
- <td
- style="
- text-align: left;
- padding: 8px;
- line-height: 1.42857143;
- vertical-align: top;
- border-top: 1px solid #ddd;
- "
- >
- <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
- </td>
- </tr>
- " }.join("\n") %>
- </tbody>
- </table>
+<h3>Pipeline Configuration:</h3>
+<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
+ <tbody style="border-bottom: 1px solid #ddd;">
+ <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
+ </tbody>
+</table>
- <p>nf-core/hic</p>
- <p><a href="https://github.com/nf-core/hic">https://github.com/nf-core/hic</a></p>
- </div>
- </body>
+<p>nf-core/hic</p>
+<p><a href="https://github.com/nf-core/hic">https://github.com/nf-core/hic</a></p>
+
+</div>
+
+</body>
</html>
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 5473b62..3652c63 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -98,7 +98,7 @@ class RowChecker:
if row[self._first_col] and row[self._second_col]:
row[self._single_col] = False
assert (
- Path(row[self._first_col]).suffixes == Path(row[self._second_col]).suffixes
+ Path(row[self._first_col]).suffixes[-2:] == Path(row[self._second_col]).suffixes[-2:]
), "FASTQ pairs must have the same file extensions."
else:
row[self._single_col] = True
@@ -129,6 +129,16 @@ class RowChecker:
row[self._sample_col] = f"{sample}_T{seen[sample]}"
+def read_head(handle, num_lines=10):
+ """Read the specified number of lines from the current position in the file."""
+ lines = []
+ for idx, line in enumerate(handle):
+ if idx == num_lines:
+ break
+ lines.append(line)
+ return "".join(lines)
+
+
def sniff_format(handle):
"""
Detect the tabular format.
@@ -144,13 +154,13 @@ def sniff_format(handle):
https://docs.python.org/3/glossary.html#term-text-file
"""
- peek = handle.read(2048)
+ peek = read_head(handle)
+ handle.seek(0)
sniffer = csv.Sniffer()
if not sniffer.has_header(peek):
logger.critical(f"The given sample sheet does not appear to contain a header.")
sys.exit(1)
dialect = sniffer.sniff(peek)
- handle.seek(0)
return dialect
diff --git a/nextflow.config b/nextflow.config
index 50a4460..7905a9a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -159,7 +159,7 @@ trace {
}
dag {
enabled = true
- file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
+ file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {
@@ -169,7 +169,7 @@ manifest {
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
- version = '1.3.1'
+ version = '1.4.0dev'
}
// Load modules.config for DSL2 module specific options
--
GitLab