diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 4d71d9a3f171658e4189107f2abc239f9f98bfa2..82c1a4ecd1bac8b5410b2825e230f9f3924594d3 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 f892cfd3f1d6deb2f2c57cd60269c51638c85dc6..5cd0714273dca87007b7c5ea50df27d05fe3606d 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 363667229e33a8fe022f697e4755d911234a12fb..b92e3d24195d72e7a4c39605fd29de3cf657bd06 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 cc0fc52d25b4945b1bf0e460f3ce6527e5cad992..0dac5c2786f66f7e503085c858823a4833afb92a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,6 +45,3 @@ jobs:
- name: Run pipeline with test data
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 0000000000000000000000000000000000000000..502eff95019714bf6b719046f0127d1e998f6b8a
--- /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 e9cf5de3ac6a3a8a41923568a170315053d7e2e0..77358dee77fafceacab736de94ae79f2258a523f 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 91c487a1a5020bf2b0ff8d31a3c2b9d589e5fed8..04758f61e368b37a7651aff015e51a9c31162542 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 0000000000000000000000000000000000000000..d0e7ae58916d32ec5fc706ae0eda9403db44f290
--- /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 3478c9d43223d5a31da6b35c737006e0a691242e..b66d2bc633650b8e74a028f5e760a79c83627dff 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).
-## v1.4.0
+## v1.4.0dev
### `Added`
diff --git a/README.md b/README.md
index 8e7f9b97c22fc4459536d5ed97acd5134277a666..48a23b070e337e18fd7ceb230d4aa802f7bdd4e5 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +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 80d5dac884d9d5032c63f7be02e8bb7c788a51d7..d207f011f3ab74ac04ace7a4e277c59900cf058a 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 17137e53b338a6a6a3e591ab1c71a5879c045994..6be15bd25d60d6901b2ff4154033e6271d9f3869 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -97,7 +97,7 @@ 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
@@ -128,6 +128,16 @@ 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.
@@ -143,13 +153,13 @@ 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 2a010be8d32879513280943f75f3a54a11555fd0..b003a2270e2297c98f77d5e204e06e3f06f0df69 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -233,7 +233,7 @@ trace {
}
dag {
enabled = true
- file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
+ file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {