Merge pull request #158 from nvnieuwk/fix/language-server

Fix/language server
nf-core · Jan 10, 2025 · cbb4b84 · cbb4b84
2 parents afd9ff2 + b422fbc
commit cbb4b84
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -105,8 +105,6 @@ jobs:
         run: |
           nf-test test \
               --ci \
-              --debug \
-              --verbose \
               --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
               --shard ${{ matrix.shard }}/5 \
               --changed-since HEAD^ \

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#144](https://github.com/nf-core/rnavar/pull/144) - Change gatk_vf params from integer to floats
 - [#145](https://github.com/nf-core/rnavar/issues/145) - Converted `star_index` and `gtf` emit channels from queue to value channels in `PREPARE_GENOME` subworkflow
 - [#149](https://github.com/nf-core/rnavar/pull/149) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf
+- [#158](https://github.com/nf-core/rnavar/pull/158) - Fixed language server errors and warnings
 
 ### Dependencies
 
@@ -54,7 +55,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | fastqc     | 0.11.9      | 0.12.1      |
 | mosdepth   | 0.3.3       | 0.3.6       |
 | multiqc    | 1.15        | 1.18        |
-| samtools   | 1.17        | 1.18        |
+| picard     | 3.1.0       | 3.3.0       |
+| samtools   | 1.17        | 1.21        |
+| star       | 2.7.10a     | 2.7.11b     |
 
 ## [1.0.0] nfcore/rnavar - 2022/06/20
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -243,41 +243,40 @@ process {
 }
 
 // BASE RECALIBRATION PROCESS
-if(!params.skip_baserecalibration) {
-    process {
-
-        withName: GATK4_BASERECALIBRATOR {
-            ext.args    =  '--use-original-qualities'
-            publishDir  = [ enabled: false ]
-        }
-
-        withName: '.*:RECALIBRATE:APPLYBQSR' {
-            ext.args    = [
-                '--use-original-qualities',
-                '--add-output-sam-program-record'
-            ].join(' ').trim()
-            ext.prefix  = {"${meta.id}.recal"}
-            publishDir  = [
-                path: { "${params.outdir}/preprocessing/${meta.id}" },
-                mode: params.publish_dir_mode,
-                enabled: true,
-                pattern: "*.{bam}"
-            ]
-        }
+process {
 
-        withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' {
-            ext.args    = params.bam_csi_index ? '-c' : ''
-            ext.prefix  = {"${meta.id}.recal"}
-            publishDir  = [
-                path: { "${params.outdir}/preprocessing/${meta.id}" },
-                mode: params.publish_dir_mode,
-                enabled: true,
-                pattern: "*.{bai,csi}"
-            ]
-        }
+    withName: GATK4_BASERECALIBRATOR {
+        ext.args    =  '--use-original-qualities'
+        publishDir  = [ enabled: false ]
+    }
+
+    withName: '.*:RECALIBRATE:APPLYBQSR' {
+        ext.args    = [
+            '--use-original-qualities',
+            '--add-output-sam-program-record'
+        ].join(' ').trim()
+        ext.prefix  = {"${meta.id}.recal"}
+        publishDir  = [
+            path: { "${params.outdir}/preprocessing/${meta.id}" },
+            mode: params.publish_dir_mode,
+            enabled: true,
+            pattern: "*.{bam}"
+        ]
+    }
+
+    withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' {
+        ext.args    = params.bam_csi_index ? '-c' : ''
+        ext.prefix  = {"${meta.id}.recal"}
+        publishDir  = [
+            path: { "${params.outdir}/preprocessing/${meta.id}" },
+            mode: params.publish_dir_mode,
+            enabled: true,
+            pattern: "*.{bai,csi}"
+        ]
     }
 }
 
+
 // VARIANT CALLING AND FILTERING
 
 process {

diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config
@@ -16,102 +16,90 @@
 process {
 
     // SNPEFF
-    if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) {
-        withName: 'SNPEFF_SNPEFF' {
-            ext.args   = { '-nodownload -canon -v' }
-            ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' }
-            publishDir = [
-                [
-                    mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
-                    pattern: "*{csv,html,genes.txt}",
-                    saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null }
-                ]
+    withName: 'SNPEFF_SNPEFF' {
+        ext.args   = { '-nodownload -canon -v' }
+        ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' }
+        publishDir = [
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
+                pattern: "*{csv,html,genes.txt}",
+                saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null }
             ]
-        }
+        ]
     }
 
     // VEP
-    if (params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge'))) {
-        withName: 'ENSEMBLVEP_VEP' {
-            ext.args   = { [
-                "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
-                (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
-                (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence)     ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"   : '',
-                (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
-                (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}"            : '',
-                (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                : '',
-                (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf',
-                (params.vep_custom_args)                                              ?: ''
-            ].join(' ').trim() }
-            // If just VEP: <vcf prefix>_VEP.ann.vcf
-            ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' }
-            publishDir = [
-                [
-                    mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" },
-                    pattern: "*html"
-                ],
-                [
-                    mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
-                    pattern: "*{gz}"
-                ]
+    withName: 'ENSEMBLVEP_VEP' {
+        ext.args   = { [
+            "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
+            (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
+            (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence)     ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"   : '',
+            (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
+            (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}"            : '',
+            (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                : '',
+            (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf',
+            (params.vep_custom_args)                                              ?: ''
+        ].join(' ').trim() }
+        // If just VEP: <vcf prefix>_VEP.ann.vcf
+        ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' }
+        publishDir = [
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" },
+                pattern: "*html"
+            ],
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
+                pattern: "*{gz}"
             ]
-        }
+        ]
     }
 
     // BCFTOOLS ANNOTATE
-    if (params.annotate_tools && params.annotate_tools.split(',').contains('bcfann')) {
-        withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
-            ext.args   = { '--output-type z' }
-            ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
-            publishDir = [
-                    mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
-                    pattern: "*{gz}"
-                ]
-        }
+    withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
+        ext.args   = { '--output-type z' }
+        ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
+        publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
+                pattern: "*{gz}"
+            ]
     }
 
     // SNPEFF THEN VEP
-    if (params.annotate_tools && params.annotate_tools.split(',').contains('merge')) {
-        withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' {
-            ext.args   = { [
-                "--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
-                (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
-                (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence)     ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"   : '',
-                (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
-                (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}"            : '',
-                (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                : '',
-                (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf',
-                (params.vep_custom_args)                                              ?: ''
-            ].join(' ').trim() }
-            // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
-            ext.prefix = { vcf.baseName - '.ann.vcf' + '_VEP.ann' }
-        }
+    withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' {
+        ext.args   = { [
+            "--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
+            (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
+            (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence)     ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"   : '',
+            (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
+            (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}"            : '',
+            (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                : '',
+            (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf',
+            (params.vep_custom_args)                                              ?: ''
+        ].join(' ').trim() }
+        // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
+        ext.prefix = { vcf.baseName - '.ann.vcf' + '_VEP.ann' }
     }
 
     // ALL ANNOTATION TOOLS
-    if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge') || params.annotate_tools.split(',').contains('bcfann'))) {
-        withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
-            ext.prefix = { input.name - '.vcf' }
-            publishDir = [
-                    mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
-                    pattern: "*{gz.tbi}"
-            ]
-        }
-    }
-
-    if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) {
-        withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' {
-            publishDir = [
+    withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
+        ext.prefix = { input.name - '.vcf' }
+        publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
-                pattern: "*{gz,gz.tbi}",
-                saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null }
-            ]
-        }
+                pattern: "*{gz.tbi}"
+        ]
+    }
+
+    withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' {
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
+            pattern: "*{gz,gz.tbi}",
+            saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null }
+        ]
     }
 }
diff --git a/main.nf b/main.nf
@@ -128,7 +128,7 @@ workflow NFCORE_RNAVAR {
         snpeff_info     = Channel.of([ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], params.snpeff_genome, params.snpeff_db ])
         DOWNLOAD_CACHE_SNPEFF_VEP(ensemblvep_info, snpeff_info)
         snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache
-        vep_cache    = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ meta, cache -> [ cache ] }
+        vep_cache    = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ _meta, cache -> [ cache ] }
 
         ch_versions = ch_versions.mix(DOWNLOAD_CACHE_SNPEFF_VEP.out.versions)
     } else {
@@ -190,10 +190,8 @@ workflow {
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
-        params.monochrome_logs,
         args,
         params.outdir,
-        params.input
     )
 
     //