diff --git a/.editorconfig b/.editorconfig
index afb20bb1ec9082b031f37fdd2c339df8c33b030e..95549501a244df9e5df775ebebc904a950fdeb38 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -11,6 +11,9 @@ indent_style = space
[*.{yml,yaml}]
indent_size = 2
+[*.json]
+insert_final_newline = unset
+
# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index c8351e2bb0a3c584c07cf391bccb2c6be68c60ce..4b432d2ac27327fac258792c6570af2149cfb053 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/hic, the standard workflow is as fo
* 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/hic repository](https://github.com/nf-core/hic) 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/).
@@ -69,7 +69,7 @@ If you wish to contribute a new step, please use the following coding standards:
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`.
@@ -83,7 +83,7 @@ If you wish to contribute a new step, please use the following coding standards:
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
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 693558cb6d3d1acc19f8625cd5407d3fae60db38..59cc2f6c6e91d3e8fc4a44fc953e7db2a3525edc 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/hic/
- [ ] 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/nf-core/hic/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/hic _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint .`).
+- [ ] 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.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index fbde5cf8b8bd03d506c3a486ac46baf7402f95b4..3b448773c4ce6da9ebd6486e5d6e33e1fd752c6d 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -53,7 +53,7 @@ jobs:
- uses: actions/setup-node@v1
with:
- node-version: "10"
+ node-version: '10'
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
diff --git a/README.md b/README.md
index ce38d720537f443a842d5fff0cfce2f7d170efd4..3dd2b4b3fe48f429a3918f596631749fec36dd95 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
## Quick Start
-1. Install [`Nextflow`](https://nf-co.re/usage/installation) (`>=21.04.0`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
index f6a861b36a065664348822185d4039f4ec556db3..322c97c6fc74194e352853b6f5c8f33827a1cbd9 100755
--- a/bin/scrape_software_versions.py
+++ b/bin/scrape_software_versions.py
@@ -30,7 +30,7 @@ for k, v in sorted(results.items()):
print(" <dt>{}</dt><dd><samp>{}</samp></dd>".format(k, v))
print(" </dl>")
-# Write out regexes as csv file:
+# Write out as tsv file:
with open("software_versions.tsv", "w") as f:
for k, v in sorted(results.items()):
f.write("{}\t{}\n".format(k, v))
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index b6e689ec883ee85fd1f884c7d9c4960062ba5db8..44551e0a3521cfd9f02501d0a4a1db460dd1ff07 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -24,17 +24,21 @@ class NfcoreTemplate {
public static void hostName(workflow, params, log) {
Map colors = logColours(params.monochrome_logs)
if (params.hostnames) {
- def hostname = "hostname".execute().text.trim()
- params.hostnames.each { prof, hnames ->
- hnames.each { hname ->
- if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
- log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
- "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
- " but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
- " ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
- "=${colors.yellow}====================================================${colors.reset}="
+ try {
+ def hostname = "hostname".execute().text.trim()
+ params.hostnames.each { prof, hnames ->
+ hnames.each { hname ->
+ if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
+ log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
+ "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
+ " but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
+ " ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
+ "=${colors.yellow}====================================================${colors.reset}="
+ }
}
}
+ } catch (Exception e) {
+ log.warn "[$workflow.manifest.name] Could not determine 'hostname' - skipping check. Reason: ${e.message}."
}
}
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c04fb92dbaf1d7b015a4c77b961cdd23c1d6c76a..f8154bdd36c9f9269222395f1cbd70b83c140cff 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -18,7 +18,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
- "pattern": "\\.csv$",
+ "pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/hic/usage#samplesheet-input).",
@@ -60,7 +60,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
- "pattern": "\\.fn?a(sta)?(\\.gz)?$",
+ "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 7e9a39cb112804fb87c7c740290e873e41bc56a7..bf53d9a547e27c726413efaf5fa51568ca6abcce 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -130,7 +130,9 @@ workflow HIC {
*/
workflow.onComplete {
- NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+ if (params.email || params.email_on_fail) {
+ NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+ }
NfcoreTemplate.summary(workflow, params, log)
}