Update all modules

CHANGELOG.md

@@ -15,12 +15,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab)
 - [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab)
 - [#38](https://github.com/qbic-pipelines/vcftomaf/pull/38) - Template update to 3.5.1 (@famosab)
+- [#39](https://github.com/qbic-pipelines/vcftomaf/pull/39) - Update all modules (@famosab)
 
 ### `Dependencies`
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| MultiQC    | 1.25.1      | 1.32        |
+| Dependency.    | Old version | New version |
+| -------------- | ----------- | ----------- |
+| BCFtools       | 1.20        | 1.22        |
+| Gunzip         | 1.1         | 1.13        |
+| MultiQC        | 1.25.1      | 1.33        |
+| Picard         | 3.3.0       | 3.4.0       |
+| Tabix (HTSlib) | 1.20        | 1.21        |
 
 ### `Deprecated`
 

conf/base.config

@@ -10,9 +10,9 @@
 
 process {
 
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus          = { 1 * task.attempt }
+    memory        = { 6.GB * task.attempt }
+    time          = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -23,43 +23,43 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withLabel:process_single {
-        cpus   = { 1                   }
+    withLabel: process_single {
+        cpus   = { 1 }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
+    withLabel: process_low {
+        cpus   = { 2 * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_medium {
-        cpus   = { 6     * task.attempt }
+    withLabel: process_medium {
+        cpus   = { 6 * task.attempt }
         memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        time   = { 8.h * task.attempt }
     }
-    withLabel:process_high {
-        cpus   = { 12    * task.attempt }
+    withLabel: process_high {
+        cpus   = { 12 * task.attempt }
         memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        time   = { 16.h * task.attempt }
     }
-    withLabel:process_long {
-        time   = { 20.h  * task.attempt }
+    withLabel: process_long {
+        time = { 20.h * task.attempt }
     }
-    withLabel:process_high_memory {
+    withLabel: process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }

conf/modules.config

@@ -15,19 +15,21 @@ process {
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
     ]
 
     withName: BCFTOOLS_VIEW {
-        ext.args = { [ "",
-            params.filter ? "-f PASS": "",
-            "--output-type z"
-            ].join(" ").trim() }
+        ext.args = {
+            [
+                "",
+                params.filter ? "-f PASS" : "",
+                "--output-type z",
+            ].join(" ").trim()
+        }
     }
 
     withName: GUNZIP {
-        publishDir        = [
-            //specify to avoid publishing, overwritten otherwise
+        publishDir = [
             enabled: false
         ]
     }
@@ -37,61 +39,61 @@ process {
             [
                 path: { "${params.outdir}/liftover/lifted/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.lifted.vcf.gz"
+                pattern: "*.lifted.vcf.gz",
             ],
             [
                 path: { "${params.outdir}/liftover/unlifted/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.unlifted.vcf.gz"
+                pattern: "*.unlifted.vcf.gz",
             ],
             [
                 path: { "${params.outdir}/liftover/logs/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
-            ]
+                pattern: "*.log",
+            ],
         ]
     }
 
     withName: TABIX_TABIX {
-        publishDir        = [
-            //specify to avoid publishing, overwritten otherwise
+        publishDir = [
             enabled: false
         ]
     }
 
     withName: UNTAR {
-        publishDir        = [
-            //specify to avoid publishing, overwritten otherwise
+        publishDir = [
             enabled: false
         ]
     }
 
     withName: VCF2MAF {
-        ext.args = { [ "",
-            params.run_vep ? "" : "--inhibit-vep",
-            meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
-            meta.tumor_id  ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}"     : "",
-            "--retain-fmt AD,AF,DP,GQ,GT,STR",
-            "--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
-            "--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
-            "--any-allele",
-            "--ncbi-build ${params.genome.tokenize('.')[-1]}",
-            "--species homo_sapiens"
-        ].join(" ").trim() }
+        ext.args   = {
+            [
+                "",
+                params.run_vep ? "" : "--inhibit-vep",
+                meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
+                meta.tumor_id ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}" : "",
+                "--retain-fmt AD,AF,DP,GQ,GT,STR",
+                "--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
+                "--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
+                "--any-allele",
+                "--ncbi-build ${params.genome.tokenize('.')[-1]}",
+                "--species homo_sapiens",
+            ].join(" ").trim()
+        }
         publishDir = [
             path: { "${params.outdir}/maf" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
-
 }

conf/test.config

@@ -14,7 +14,7 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '15.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
@@ -23,10 +23,9 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input        = "${projectDir}/tests/samplesheets/samplesheet.csv"
-    fasta        = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
-    intervals    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
-    genome       = 'GATK.GRCh38'
-    filter       = false
-
+    input                      = "${projectDir}/tests/samplesheets/samplesheet.csv"
+    fasta                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    intervals                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
+    genome                     = 'GATK.GRCh38'
+    filter                     = false
 }

main.nf

@@ -17,6 +17,46 @@ include { VCFTOMAF                } from './workflows/vcftomaf'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN MAIN WORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow {
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION(
+        params.version,
+        params.validate_params,
+        params.monochrome_logs,
+        args,
+        params.outdir,
+        params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden,
+    )
+
+    //
+    // WORKFLOW: Run main workflow
+    //
+    QBICPIPELINES_VCFTOMAF(
+        PIPELINE_INITIALISATION.out.samplesheet
+    )
+
+    //
+    PIPELINE_COMPLETION(
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        QBICPIPELINES_VCFTOMAF.out.multiqc_report,
+    )
+}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -28,97 +68,42 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcft
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
 workflow QBICPIPELINES_VCFTOMAF {
-
     take:
     samplesheet // channel: samplesheet read in from --input
 
     main:
-
     //
     // SET PARAMETERS
     //
     params.fasta = getGenomeAttribute('fasta')
     params.dict = getGenomeAttribute('dict')
 
     // Extra files
-    intervals      = params.intervals      ? Channel.fromPath(params.intervals).collect()      : Channel.value([])
-    liftover_chain = params.liftover_chain ? Channel.fromPath(params.liftover_chain).collect() : Channel.value([])
+    intervals = params.intervals ? channel.fromPath(params.intervals).collect() : channel.value([])
+    liftover_chain = params.liftover_chain ? channel.fromPath(params.liftover_chain).collect() : channel.value([])
 
     // FASTA
-    fasta        = params.fasta     ? Channel.fromPath(params.fasta).collect()          : Channel.value([])
-    dict         = params.dict      ? Channel.fromPath(params.dict).collect()           : Channel.empty()
-
-    // Genome version
-    genome        = params.genome   ?: Channel.empty()
+    fasta = params.fasta ? channel.fromPath(params.fasta).collect() : channel.value([])
+    dict = params.dict ? channel.fromPath(params.dict).collect() : channel.empty()
 
     // VEP cache
-    vep_cache          = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
-    vep_cache_unpacked = Channel.value([])
-
+    vep_cache = params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([])
+    vep_cache_unpacked = channel.value([])
 
     //
     // WORKFLOW: Run pipeline
     //
 
-    VCFTOMAF (
+    VCFTOMAF(
         samplesheet,
         intervals,
         fasta,
         dict,
         liftover_chain,
-        genome,
         vep_cache,
-        vep_cache_unpacked
+        vep_cache_unpacked,
     )
 
     emit:
     multiqc_report = VCFTOMAF.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow {
-
-    main:
-    //
-    // SUBWORKFLOW: Run initialisation tasks
-    //
-    PIPELINE_INITIALISATION (
-        params.version,
-        params.validate_params,
-        params.monochrome_logs,
-        args,
-        params.outdir,
-        params.input,
-        params.help,
-        params.help_full,
-        params.show_hidden
-    )
-
-    //
-    // WORKFLOW: Run main workflow
-    //
-    QBICPIPELINES_VCFTOMAF (
-        PIPELINE_INITIALISATION.out.samplesheet
-    )
-
-    //
-    PIPELINE_COMPLETION (
-        params.email,
-        params.email_on_fail,
-        params.plaintext_email,
-        params.outdir,
-        params.monochrome_logs,
-        params.hook_url,
-        QBICPIPELINES_VCFTOMAF.out.multiqc_report
-    )
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/