Merge branch 'dsl2' into dsl2_csv_magic

.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

.github/CONTRIBUTING.md

@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/sarek, the standard workflow is as
     * 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/sarek repository](https://github.com/nf-core/sarek) 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
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare
 - [ ] 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/sarek/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/sarek _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.

.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

README.md

@@ -44,7 +44,7 @@ By default, the pipeline currently performs the following:
 
 ## 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))_
 

bin/scrape_software_versions.py

@@ -30,7 +30,7 @@
     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))

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}."
             }
         }
     }

nextflow_schema.json

@@ -19,7 +19,7 @@
                     "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 a header row. See [usage docs](https://nf-co.re/sarek/usage#input).",
@@ -443,7 +443,7 @@
                     "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"

workflows/sarek.nf

@@ -497,6 +497,13 @@ workflow SAREK {
     ch_software_versions = ch_software_versions.mix(MULTIQC.out.version.ifEmpty(null))
 }
 
+workflow.onComplete {
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    }
+    NfcoreTemplate.summary(workflow, params, log)
+}
+
 // Function to extract information (meta data + file(s)) from csv file(s)
 def extract_csv(csv_file) {
     Channel.from(csv_file).splitCsv(header: true)