diff --git a/CHANGELOG.md b/CHANGELOG.md index 682a676521..ee162a03fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ - Use `params.monochrome_logs` in the template and update nf-core components ([#3310](https://github.com/nf-core/tools/pull/3310)) - Fix some typos and improve writing in `usage.md` and `CONTRIBUTING.md` ([#3302](https://github.com/nf-core/tools/pull/3302)) - Add `manifest.contributors` to `nextflow.config` ([#3311](https://github.com/nf-core/tools/pull/3311)) +- Update template components ([#3328](https://github.com/nf-core/tools/pull/3328)) ### Download diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index b8165fbc06..67d24ff0f7 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -8,4 +8,4 @@ tasks: vscode: extensions: #{%- if code_linters -%} - - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack + - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack{% endif %} diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 397c0cdb03..7d2761d290 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -28,7 +28,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "85400682a2abac63b09c863c138e91e5df7236b5", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", "installed_by": ["subworkflows"] }{% if nf_schema %}, "utils_nfschema_plugin": { diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 228dbff897..bfd258760d 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -203,29 +203,24 @@ def logColours(monochrome_logs=true) { return colorcodes } +// Return a single report from an object that may be a Path or List // -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] - } +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - catch (Exception msg) { - log.debug(msg) - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } - } - return mqc_report } // @@ -279,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -310,7 +305,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi if (email_address) { try { if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -318,7 +314,7 @@ new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } catch (Exception msg) { - log.debug(msg) + log.debug(msg.toString()) log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index e43d208b1b..f117040cbd 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -79,4 +79,48 @@ nextflow_function { ) } } + + test("Test Function getSingleReport with a single file") { + function "getSingleReport" + + when { + function { + """ + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert function.result.contains("test.tsv") } + ) + } + } + + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" + + when { + function { + """ + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } + ) + } + } }