Update nf-tests and language server fixes

conf/test_full.config

@@ -35,10 +35,10 @@ params {
 
     // Panelprep optional args
     remove_samples = "NA12878,NA12891,NA12892"
-    normalize      = true
-    compute_freq   = true
-    phase          = true
+    normalize      = false
+    compute_freq   = false
+    phase          = false
 
     // Impute tools
-    tools = "glimpse1"
+    tools = "glimpse2"
 }

docs/usage.md

@@ -278,7 +278,7 @@ For starting from the imputation steps, the required flags are:
 
 Here is a representation on how the input files will be processed depending on the input files type and the selected imputation tool.
 
-[![InputSoftwareCompatibility](images/InputSoftware_compatibility.png)](images/InputSoftware_compatibility.png)
+![InputSoftwareCompatibility](images/InputSoftware_compatibility.png)
 
 #### Argument `--batch_size`
 

modules/local/bam_chr_extract/main.nf

@@ -35,7 +35,6 @@ process BAM_CHR_EXTRACT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

modules/local/vcf_chr_extract/main.nf

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

subworkflows/local/bam_chr_rename_samtools/main.nf

@@ -13,6 +13,7 @@ workflow BAM_CHR_RENAME_SAMTOOLS {
     SAMTOOLS_REHEADER(
         ch_bam.map{
             meta, bam, index, prefix ->
+            def cmd = ""
             if (prefix == "nochr") {
                 cmd = 'sed -E "s/^(@SQ.*\\tSN:)chr/\\1/"'
             } else if (prefix == "chr") {

subworkflows/local/bam_impute_quilt/main.nf

@@ -18,12 +18,12 @@ workflow BAM_IMPUTE_QUILT {
     posfile_phasefile   = [[id: null], posfile, phasefile]
     genetic_map_file    = []
 
-    ngen                = params.ngen
-    buffer              = params.buffer
+    ngen_params         = params.ngen
+    buffer_params       = params.buffer
 
     ch_hap_chunks = ch_hap_legend
         .combine(ch_chunks, by:0)
-        .map { it + ngen + buffer + [[]] }
+        .map { it + ngen_params + buffer_params + [[]] }
 
     if (!genetic_map_file.isEmpty()) {
         // Add genetic map file (untested)

subworkflows/local/bam_impute_stitch/main.nf

@@ -19,8 +19,8 @@ workflow BAM_IMPUTE_STITCH {
     // Value channels
     def input_empty         = [[]]
     def rdata_empty         = [[]]
-    k_val                   = params.k_val
-    ngen                    = params.ngen
+    k_val_params            = params.k_val
+    ngen_params             = params.ngen
 
     // Transform posfile to TSV with ','
     GAWK(ch_posfile, [])
@@ -38,7 +38,7 @@ workflow BAM_IMPUTE_STITCH {
     ch_parameters = ch_posfile
         .map { it + input_empty + rdata_empty}
         .join(ch_chromosomes)
-        .map { it + k_val + ngen}
+        .map { it + k_val_params + ngen_params}
         .map { metaC, metaPC, posfile, input, rdata, chr, k_val, ngen ->
             [metaPC, posfile, input, rdata, chr, k_val, ngen]
         }

subworkflows/local/bam_impute_stitch/tests/main.nf.test

@@ -16,12 +16,14 @@ nextflow_workflow {
     tag "bcftools_index"
 
     test("Prepare input stitch") {
-        setup {
-            run("PREPARE_INPUT_STITCH") {
-                script "../../prepare_input_stitch/main.nf"
-                process {
-                    """
-                    input[0] = Channel.fromList([
+        when {
+            params {
+                max_cpus   = 2
+                max_memory = '2.GB'
+            }
+            workflow {
+                """
+                ch_samples = Channel.fromList([
                         [
                             [id: "NA12878"],
                             file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s.bam", checkIfExist:true),
@@ -33,27 +35,21 @@ nextflow_workflow {
                             file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExist:true),
                         ],
                     ])
-                    input[1] = Channel.of([
-                            [id: "1000GP", chr: "chr22"],
-                            file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.legend.gz", checkIfExist:true)
-                        ]).collect()
-                    input[2] = Channel.of([
-                        [chr: "chr22", region: "chr22:16570000-16610000"], "chr22:16570000-16610000"
-                    ]).collect()
-                    """
-                }
-            }
-        }
-        when {
-            params {
-                max_cpus   = 2
-                max_memory = '2.GB'
-            }
-            workflow {
-                """
-                input[0] = PREPARE_INPUT_STITCH.out.stitch_samples
-                input[1] = PREPARE_INPUT_STITCH.out.stitch_parameters
-                input[2] = Channel.of([
+                bamlist  = Channel.of("NA12878.s.bam", "NA19401.s.bam").collectFile(name: "bamlist")
+
+                ch_posfile = Channel.of([
+                    [id: "1000GP", chr: "chr22"],
+                    file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.legend.gz", checkIfExist:true)
+                ])
+
+                ch_region = Channel.of([
+                    [chr: "chr22", region: "chr22:16570000-16610000"], "chr22:16570000-16610000"
+                ])
+
+                input[0] = ch_samples.combine(bamlist)
+                input[1] = ch_posfile
+                input[2] = ch_region
+                input[3] = Channel.of([
                     [id: "GRCh38"],
                     file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz", checkIfExist:true),
                     file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz.fai", checkIfExist:true),

subworkflows/local/utils_nfcore_chrcheck_pipeline/main.nf

@@ -2,7 +2,7 @@
 // Check if the contig names in the input files match the reference contig names.
 //
 def checkChr(ch_chr, ch_input){
-    chr_checked = ch_chr
+    def chr_checked = ch_chr
         .combine(ch_input, by:0)
         .map{meta, chr, file, index, lst ->
             [
@@ -12,9 +12,9 @@ def checkChr(ch_chr, ch_input){
             ]
         }
         .branch{ meta, file, index, chr, lst ->
-            lst_diff = diffChr(chr, lst, file)
-            diff = lst_diff[0]
-            prefix = lst_diff[1]
+            def lst_diff = diffChr(chr, lst, file)
+            def diff = lst_diff[0]
+            def prefix = lst_diff[1]
             no_rename: diff.size() == 0
                 return [meta, file, index]
             to_rename: true
@@ -27,22 +27,22 @@ def checkChr(ch_chr, ch_input){
 // Check if the contig names can be solved by adding/removing the `chr` prefix.
 //
 def diffChr(chr_target, chr_ref, file) {
-    diff = chr_ref - chr_target
-    prefix = (chr_ref - chr_target) =~ "chr" ? "chr" : "nochr"
+    def diff = chr_ref - chr_target
+    def prefix = (chr_ref - chr_target) =~ "chr" ? "chr" : "nochr"
     if (diff.size() != 0) {
         // Ensure that by adding/removing the prefix we can solve the problem
-        new_chr = []
-        to_rename = []
+        def new_chr = []
+        def to_rename = []
         if (prefix == "chr") {
             chr_target.each{ new_chr += "chr${it}" }
             diff.each{ to_rename += it.replace('chr', '') }
         } else {
             chr_target.each{ new_chr += it.replace('chr', '') }
             diff.each{ to_rename += "chr${it}" }
         }
-        new_diff = diff - new_chr
+        def new_diff = diff - new_chr
         if (new_diff.size() != 0) {
-            chr_names = new_diff.size() > params.max_chr_names ? new_diff[0..params.max_chr_names - 1] + ['...'] : new_diff
+            def chr_names = new_diff.size() > params.max_chr_names ? new_diff[0..params.max_chr_names - 1] + ['...'] : new_diff
             error "Contig names: ${chr_names} absent from file: ${file} and cannot be solved by adding or removing the `chr` prefix."
         }
         diff = to_rename

subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf

@@ -351,40 +351,40 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters() {
     genomeExistsError()
     // Check that only genome or fasta is provided
-    assert params.genome == null || params.fasta == null, "Either --genome or --fasta must be provided"
-    assert !(params.genome == null && params.fasta == null), "Only one of --genome or --fasta must be provided"
+    assert (params.genome == null || params.fasta == null) : "Either --genome or --fasta must be provided"
+    assert !(params.genome == null && params.fasta == null) : "Only one of --genome or --fasta must be provided"
 
     // Check that a steps is provided
-    assert params.steps, "A step must be provided"
+    assert params.steps : "A step must be provided"
 
     // Check that at least one tool is provided
     if (params.steps.split(',').contains("impute")) {
-        assert params.tools, "No tools provided"
+        assert params.tools : "No tools provided"
     }
 
     // Check that input is provided for all steps, except panelprep
     if (params.steps.split(',').contains("all") || params.steps.split(',').contains("impute") || params.steps.split(',').contains("simulate") || params.steps.split(',').contains("validate")) {
-        assert params.input, "No input provided"
+        assert params.input : "No input provided"
     }
 
     // Check that posfile and chunks are provided when running impute only. Steps with panelprep generate those files.
     if (params.steps.split(',').contains("impute") && !params.steps.split(',').find { it in ["all", "panelprep"] }) {
         // Required by all tools except glimpse2
         if (!params.tools.split(',').find { it in ["glimpse2"] }) {
-                assert params.posfile, "No --posfile provided for --steps impute"
+                assert params.posfile : "No --posfile provided for --steps impute"
         }
         // Required by all tools except STITCH
         if (params.tools != "stitch") {
-                assert params.chunks, "No --chunks provided for --steps impute"
+                assert params.chunks : "No --chunks provided for --steps impute"
         }
         // Required by GLIMPSE1 and GLIMPSE2 only
         if (params.tools.split(',').contains("glimpse")) {
-                assert params.panel, "No --panel provided for imputation with GLIMPSE"
+                assert params.panel : "No --panel provided for imputation with GLIMPSE"
         }
 
         // Check that input_truth is provided when running validate
         if (params.steps.split(',').find { it in ["all", "validate"] } ) {
-            assert params.input_truth, "No --input_truth was provided for --steps validate"
+            assert params.input_truth : "No --input_truth was provided for --steps validate"
         }
     }
 
@@ -492,21 +492,24 @@ def checkMetaChr(chr_a, chr_b, name){
 //
 // Get file extension
 //
+import nextflow.file.http.XPath
+import java.nio.file.Path
+
 def getFileExtension(file) {
-    if (file instanceof Path) {
-        file = file.getName()
-    } else if (file instanceof ArrayList) {
-        if (file.size() == 0) {
-            return null
-        } else {
-            error "Type not supported: ${file} = ${file.getClass()}"
-        }
-    }
-    if (file instanceof CharSequence) {
-        return file.toString().replace(".gz", "").split("\\.").last()
+    def file_name = ""
+
+    if (file instanceof Path || file instanceof XPath) {
+        file_name = file.name
+    } else if (file instanceof CharSequence) {
+        file_name = file.toString()
+    } else if (file instanceof List) {
+        return file.collect { getFileExtension(it) }
     } else {
         error "Type not supported: ${file.getClass()}"
     }
+
+    // Remove .gz if present and get the last part after splitting by "."
+    return file_name.replace(".gz", "").split("\\.").last()
 }
 
 //