Remove import statements from pipeline template

[ewels]

We should not use Groovy import statements in Nextflow files:

tools/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf

Lines 5 to 7 in 930ece5

	import org.yaml.snakeyaml.Yaml
	import groovy.json.JsonOutput
	import nextflow.extension.FilesEx

tools/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf

Lines 5 to 6 in 930ece5

	import org.yaml.snakeyaml.Yaml
	import nextflow.extension.FilesEx

Instead, use fully qualified names. So instead of:

tools/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf

Line 93 in 930ece5

Yaml parser = new Yaml()

Do this:

    Yaml parser = new org.yaml.snakeyaml.Yaml()

These are subworkflows, so need changing upstream. But adding the issue here because we need to make sure that the updated modules are pulled back into the template.

[ewels]

Related - these additional fixes are also needed to get ahead of upcoming Nextflow syntax changes:

diff --git a/subworkflows/local/utils_nfcore_test_pipeline/main.nf b/subworkflows/local/utils_nfcore_test_pipeline/main.nf
index 12c3177..ad046d5 100644
--- a/subworkflows/local/utils_nfcore_test_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_test_pipeline/main.nf
@@ -84,8 +84,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map {
-            validateInputSamplesheet(it)
+        .map {samplesheet ->
+            validateInputSamplesheet(samplesheet)
         }
         .map {
             meta, fastqs ->
@@ -165,7 +165,7 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    def endedness_ok = metas.collect{meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
@@ -238,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"