Fix language server errors

modules/nf-core/bowtie2/align/main.nf

@@ -90,7 +90,6 @@ process BOWTIE2_ALIGN {
     } else {
         create_unmapped = save_unaligned ? "touch ${prefix}.unmapped_1.fastq.gz && touch ${prefix}.unmapped_2.fastq.gz" : ""
     }
-    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
     if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
 
     def create_index = ""

modules/nf-core/bwa/index/main.nf

@@ -11,8 +11,8 @@ process BWA_INDEX {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path(bwa) , emit: index
-    path "versions.yml"        , emit: versions
+    tuple val(meta), path("bwa")  , emit: index
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/bwa/index/meta.yml

@@ -31,9 +31,12 @@ output:
           description: |
             Groovy Map containing reference information.
             e.g. [ id:'test', single_end:false ]
+          pattern: "*.{amb,ann,bwt,pac,sa}"
       - bwa:
-          type: file
-          description: BWA genome index files
+          type: map
+          description: |
+            Groovy Map containing reference information.
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.{amb,ann,bwt,pac,sa}"
   - versions:
       - versions.yml:

modules/nf-core/bwa/mem/main.nf

@@ -53,10 +53,8 @@ process BWA_MEM {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def samtools_command = sort_bam ? 'sort' : 'view'
     def extension = args2.contains("--output-fmt sam")   ? "sam" :
                     args2.contains("--output-fmt cram")  ? "cram":
                     sort_bam && args2.contains("-O cram")? "cram":

modules/nf-core/bwamem2/mem/main.nf

@@ -56,14 +56,11 @@ process BWAMEM2_MEM {
 
     stub:
 
-    def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def samtools_command = sort_bam ? 'sort' : 'view'
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
     def extension_matcher =  (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
     if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
 
     def create_index = ""

modules/nf-core/dragmap/align/main.nf

@@ -55,15 +55,11 @@ process DRAGMAP_ALIGN {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
-    def samtools_command = sort_bam ? 'sort' : 'view'
     def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
     def extension_matcher =  (args2 =~ extension_pattern)
     def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
-    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
     if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
 
     def create_index = ""

modules/nf-core/gridss/gridss/tests/main.nf.test.snap

@@ -67,17 +67,5 @@
             "nextflow": "24.04.2"
         },
         "timestamp": "2024-07-10T11:48:45.270441"
-    },
-    "human - bam - assembly": {
-        "content": [
-            [
-                "versions.yml:md5,139867df5d7eaf22a89ae574f08e8d80"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-07-09T14:13:21.550069"
     }
-}
+}

modules/nf-core/md5sum/main.nf

@@ -47,7 +47,6 @@ process MD5SUM {
     }
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if ( as_separate_files ) {
         """

modules/nf-core/samtools/coverage/main.nf

@@ -37,7 +37,6 @@ process SAMTOOLS_COVERAGE {
     """
 
     stub:
-    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

modules/nf-core/samtools/flagstat/main.nf

@@ -18,7 +18,6 @@ process SAMTOOLS_FLAGSTAT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     samtools \\

modules/nf-core/samtools/getrg/main.nf

@@ -19,7 +19,6 @@ process SAMTOOLS_GETRG {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     samtools \\
         view \\

modules/nf-core/samtools/idxstats/main.nf

@@ -18,7 +18,6 @@ process SAMTOOLS_IDXSTATS {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/nf-core/samtools/import/main.nf

@@ -46,7 +46,6 @@ process SAMTOOLS_IMPORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/nf-core/samtools/mpileup/main.nf

@@ -20,7 +20,7 @@ process SAMTOOLS_MPILEUP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def intervals = intervals ? "-l ${intervals}" : ""
+    intervals = intervals ? "-l ${intervals}" : ""
     """
     samtools mpileup \\
         --fasta-ref $fasta \\

modules/nf-core/samtools/reheader/main.nf

@@ -36,7 +36,6 @@ process SAMTOOLS_REHEADER {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam

modules/nf-core/samtools/stats/main.nf

@@ -19,7 +19,6 @@ process SAMTOOLS_STATS {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
     """

modules/nf-core/samtools/view/main.nf

@@ -63,7 +63,7 @@ process SAMTOOLS_VIEW {
                 input.getExtension()
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
-    def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
+    index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
 
     """
     touch ${prefix}.${file_type}

subworkflows/nf-core/bcl_demultiplex/main.nf

@@ -22,7 +22,7 @@ workflow BCL_DEMULTIPLEX {
         // Split flowcells into separate channels containing run as tar and run as path
         // https://nextflow.slack.com/archives/C02T98A23U7/p1650963988498929
         ch_flowcell
-            .branch { meta, samplesheet, run ->
+            .branch { _meta, _samplesheet, run ->
                 tar: run.toString().endsWith(".tar.gz")
                 dir: true
             }.set { ch_flowcells }
@@ -88,18 +88,18 @@ workflow BCL_DEMULTIPLEX {
                 line = line.substring(1)
                 // expected format is like:
                 // xx:yy:FLOWCELLID:LANE:... (seven fields)
-                fields = line.split(':')
+                def fields = line.split(':')
                 // CASAVA 1.8+ format, from  https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm
                 // "@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos>:<UMI> <read>:<is filtered>:<control number>:<index>"
-                sequencer_serial = fields[0]
-                run_nubmer       = fields[1]
-                fcid             = fields[2]
-                lane             = fields[3]
-                index            = fields[-1] =~ /[GATC+-]/ ? fields[-1] : ""
-                ID = [fcid, lane].join(".")
-                PU = [fcid, lane, index].findAll().join(".")
-                PL = "ILLUMINA"
-                SM = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/
+                //def sequencer_serial = fields[0]
+                //def run_nubmer       = fields[1]
+                def fcid             = fields[2]
+                def lane             = fields[3]
+                def index            = fields[-1] =~ /[GATC+-]/ ? fields[-1] : ""
+                def ID = [fcid, lane].join(".")
+                def PU = [fcid, lane, index].findAll().join(".")
+                def PL = "ILLUMINA"
+                def SM = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/
                 meta.readgroup = [
                     "ID": ID,
                     "SM": SM,

subworkflows/nf-core/fastq_align_dna/main.nf

@@ -29,37 +29,36 @@ workflow FASTQ_ALIGN_DNA {
         ch_versions     = Channel.empty()
 
         // Align fastq files to reference genome and (optionally) sort
-        switch (aligner) {
-            case 'bowtie2':
+        if (aligner == 'bowtie2') {
                 BOWTIE2_ALIGN(ch_reads, ch_aligner_index, ch_fasta, false, sort) // if aligner is bowtie2
                 ch_bam = ch_bam.mix(BOWTIE2_ALIGN.out.bam)
                 ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)
-                break
-            case 'bwamem':
+        }
+        else if (aligner == 'bwamem'){
                 BWAMEM1_MEM  (ch_reads, ch_aligner_index, ch_fasta, sort)        // If aligner is bwa-mem
                 ch_bam = ch_bam.mix(BWAMEM1_MEM.out.bam)
                 ch_bam_index = ch_bam_index.mix(BWAMEM1_MEM.out.csi)
                 ch_versions = ch_versions.mix(BWAMEM1_MEM.out.versions)
-                break
-            case 'bwamem2':
+        }
+        else if (aligner == 'bwamem2'){
                 BWAMEM2_MEM  (ch_reads, ch_aligner_index, ch_fasta, sort)       // If aligner is bwa-mem2
                 ch_bam = ch_bam.mix(BWAMEM2_MEM.out.bam)
                 ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions)
-                break
-            case 'dragmap':
+        }
+        else if (aligner == 'dragmap'){
                 DRAGMAP_ALIGN(ch_reads, ch_aligner_index, ch_fasta, sort)       // If aligner is dragmap
                 ch_bam = ch_bam.mix(DRAGMAP_ALIGN.out.bam)
                 ch_reports = ch_reports.mix(DRAGMAP_ALIGN.out.log)
                 ch_versions = ch_versions.mix(DRAGMAP_ALIGN.out.versions)
-                break
-            case 'snap':
-                SNAP_ALIGN   (ch_reads, ch_aligner_index)                       // If aligner is snap
-                ch_bam = ch_bam.mix(SNAP_ALIGN.out.bam)
-                ch_bam_index.mix(SNAP_ALIGN.out.bai)
-                ch_versions = ch_versions.mix(SNAP_ALIGN.out.versions)
-                break
-            default:
-                error "Unknown aligner: ${aligner}"
+        }
+        else if (aligner == 'snap'){
+            SNAP_ALIGN   (ch_reads, ch_aligner_index)                       // If aligner is snap
+            ch_bam = ch_bam.mix(SNAP_ALIGN.out.bam)
+            ch_bam_index.mix(SNAP_ALIGN.out.bai)
+            ch_versions = ch_versions.mix(SNAP_ALIGN.out.versions)
+        }
+        else {
+            error "Unknown aligner: ${aligner}"
         }
 
     emit: