Module language server fixes

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#591](https://github.com/genomic-medicine-sweden/nallo/pull/591) - Updated version to 0.6.0dev
+- [#592](https://github.com/genomic-medicine-sweden/nallo/pull/592) - Updated local and nf-core modules to fix Nextflow language server issues
 
 ### `Removed`
 

modules.json

@@ -58,7 +58,7 @@
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "ede1e20af42e2f736638efae1b79762293a6a98a",
                         "installed_by": ["modules"]
                     },
                     "bedtools/merge": {
@@ -162,7 +162,7 @@
                     },
                     "longphase/phase": {
                         "branch": "master",
-                        "git_sha": "22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c",
+                        "git_sha": "f303120bb5ee191c815bc7a756ab57576afe4c90",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
@@ -229,7 +229,7 @@
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "b21df1b4e806f7bf3aff0eb41d84453a0025b43e",
                         "installed_by": ["modules"]
                     },
                     "severus": {
@@ -267,7 +267,7 @@
                     },
                     "svdb/merge": {
                         "branch": "master",
-                        "git_sha": "a8ad84b7ee0cda0b001490e95d9ed277e687e368",
+                        "git_sha": "95185f269ec10a33cde61d294fcd4ba7c66bc6b8",
                         "installed_by": ["modules"]
                     },
                     "svdb/query": {

modules/local/create_pedigree_file/main.nf

@@ -24,11 +24,10 @@ process CREATE_PEDIGREE_FILE {
         a.family_id <=> b.family_id ?: a.id <=> b.id } : sample_metas
     outfile_text = ['#family_id', 'sample_id', 'father', 'mother', 'sex', 'phenotype'].join('\\t')
     def samples_list = []
-    for(int i = 0; i<samples.size(); i++) {
-        sample_name = samples[i].id
-        if (!samples_list.contains(sample_name)) {
-            outfile_text += "\\n" + [samples[i].family_id, sample_name, samples[i].paternal_id, samples[i].maternal_id, samples[i].sex, samples[i].phenotype].join('\\t')
-            samples_list.add(sample_name)
+    samples.each { sample ->
+        if (!samples_list.contains(sample.id)) {
+            outfile_text += "\\n" + [sample.family_id, sample.id, sample.paternal_id, sample.maternal_id, sample.sex, sample.phenotype].join('\\t')
+            samples_list.add(sample.id)
         }
     }
     """

modules/local/create_pedigree_file/tests/main.nf.test

@@ -14,7 +14,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(
-                    [ 'project',
+                    [ [ 'id': 'project' ],
                     [
                         [id:'HG002.Revio', family_id:'family', paternal_id:0, maternal_id:0, sex:0, phenotype:2, project:'project', n_files:1, single_end:true]
                     ]
@@ -40,7 +40,7 @@ nextflow_process {
             process {
                 """
                 input[0] = Channel.of(
-                    [ 'test',
+                    [ [ 'id': 'test' ],
                     [
                         [id:'HG002_Revio_AB', family_id:'FAM2', paternal_id:0, maternal_id:0, sex:0, phenotype:1, project:'test', n_files:1, single_end:true],
                         [id:'HG002_Revio_AA', family_id:'FAM2', paternal_id:0, maternal_id:0, sex:0, phenotype:1, project:'test', n_files:1, single_end:true],
@@ -64,4 +64,29 @@ nextflow_process {
         }
     }
 
+    test("create_pedigree_file - one sample -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [ [ 'id': 'project' ],
+                    [
+                        [id:'HG002.Revio', family_id:'family', paternal_id:0, maternal_id:0, sex:0, phenotype:2, project:'project', n_files:1, single_end:true]
+                    ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }

modules/local/echtvar/anno/main.nf

@@ -16,16 +16,16 @@ process ECHTVAR_ANNO {
     task.ext.when == null || task.ext.when
 
     script:
-    def args    = task.ext.args ?: ''
-    prefix      = task.ext.prefix ?: "${meta.id}"
-
-    modifiedList = []
-    for (element in databases) {
-        modifiedList.add("-e")
-        modifiedList.add(element)
-    }
+    def args  = task.ext.args ?: ''
+    prefix    = task.ext.prefix ?: "${meta.id}"
+    def input = databases.collectMany { file -> ["-e", file] }.join(" ")
     """
-    echtvar anno ${args} ${modifiedList.join(" ")} ${vcf} ${prefix}.bcf.gz
+    echtvar \\
+        anno \\
+        ${args} \\
+        ${input} \\
+        ${vcf} \\
+        ${prefix}.bcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/hiphase/main.nf

@@ -35,31 +35,31 @@ process HIPHASE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def vcfInputs = []
-    def vcfOutputs = []
+    def bamNames = []
     def vcfNames = []
-    for (vcf in vcfs) {
-        vcfInputs.add('--vcf')
-        vcfInputs.add(vcf)
-        vcfOutputs.add('--output-vcf')
-        vcfOutputs.add("${prefix}_phased.vcf.gz")
 
+    def vcfs_input = vcfs.collectMany { file ->
+        [
+            "--vcf",
+            file,
+            "--output-vcf",
+            "${prefix}_phased.vcf.gz"
+        ] }.join(" ")
+
+    def bams_input = bams.collectMany { file ->
+        [
+            "--bam",
+            file,
+            output_bam ? '--output-bam' : '',
+            output_bam ? "${prefix}_haplotagged.bam" : ''
+        ] }.join(" ")
+
+    vcfs.each { vcf ->
         vcfNames.add(vcf.getName())
     }
 
-    def bamInputs = []
-    def bamOutputs = []
-    def bamNames = []
-    for (bam in bams) {
-        bamInputs.add('--bam')
-        bamInputs.add("${bam}")
-
+    bams.each { bam ->
         bamNames.add(bam.getName())
-
-        if(output_bam) {
-            bamOutputs.add('--output-bam')
-            bamOutputs.add("${prefix}_haplotagged.bam")
-        }
     }
 
     def uniqueVcfNames = new HashSet(vcfNames);
@@ -79,10 +79,8 @@ process HIPHASE {
         $args \
         --threads ${task.cpus} \\
         --reference ${fasta} \\
-        ${bamInputs.join(' ')} \\
-        ${bamOutputs.join(' ')} \\
-        ${vcfInputs.join(' ')} \\
-        ${vcfOutputs.join(' ')}
+        ${bams_input} \\
+        ${vcfs_input}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":