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SusiJoSusiJo
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Merge remote-tracking branch 'origin/dev' into multiqc_channels
2 parents cbe9755 + e5a4ffb commit d83794f

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‎CHANGELOG.md‎

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@@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--snpeff_version` to allow more configuration on the snpeff container definition
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- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--vep_include_fasta` to use the fasta file for annotation
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- [#639](https://github.com/nf-core/sarek/pull/639) - Adding genes-txt-file and summary-html-file to the published output from snpEff.
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- [#647](https://github.com/nf-core/sarek/pull/647) - Update resource requests for preprocessing based on what worked for 5 ICGC matched WGS samples
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- [#652](https://github.com/nf-core/sarek/pull/652) - Added full size somatic test profile.
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### Changed
@@ -89,11 +90,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file
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- [#632](https://github.com/nf-core/sarek/pull/632) - Update `snpEff` version to `5.1` and cache up to `105`
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- [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
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- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
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- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
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- [#633](https://github.com/nf-core/sarek/pull/633) - Update `BCFTOOLS` version to `1.15.1`
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- [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
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- [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
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- [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`
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- [#649](https://github.com/nf-core/sarek/pull/649) - Update, simplify and add more files to all `test_*.yml` files
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- [#651](https://github.com/nf-core/sarek/pull/651) - Added TIDDIT_SOMATIC subworkflow
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- [#653](https://github.com/nf-core/sarek/pull/653) - Coherent results subfolder structure between preprocessing, variantcalling and reporting
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- [#659](https://github.com/nf-core/sarek/pull/659) - Update usage.md docu section on `How to run ASCAT with WES`
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- [#663](https://github.com/nf-core/sarek/pull/663) - Add separate parameters for `ASCAT` and `ControlFREEC` back in
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### Fixed
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@@ -143,6 +150,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#642](https://github.com/nf-core/sarek/pull/642) - Only unzip ref files if tool is run, only publish ref files if `--save_reference` and simplify CNKit logic
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- [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks
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- [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files
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- [#658](https://github.com/nf-core/sarek/pull/658) - Fix split fastq names in multiqc-report
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- [#666](https://github.com/nf-core/sarek/pull/666) - Simplify multiqc config channel input
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### Deprecated

‎assets/multiqc_config.yml‎

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@@ -59,6 +59,10 @@ extra_fn_clean_exts:
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pattern: "^.*.(md|recal).mosdepth.(global|region).dist"
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module: mosdepth
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sample_names_replace_regex: True
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sample_names_replace:
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".[0-9]{4}": ".md"
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sp:
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snpeff:
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contents: "SnpEff_version"

‎conf/base.config‎

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@@ -49,8 +49,28 @@ process {
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errorStrategy = 'retry'
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maxRetries = 2
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}
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withName: 'BWAMEM2_MEM' {
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memory = { check_max( 60.GB * task.attempt, 'memory' ) }
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withName: 'BWAMEM1_MEM|BWAMEM2_MEM' {
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cpus = { check_max( 24 * task.attempt, 'cpus' ) }
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memory = { check_max( 36.GB * task.attempt, 'memory' ) }
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time = { check_max( 48.h * task.attempt, 'time' ) }
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}
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withName: 'FASTP'{
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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}
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withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT|SAMTOOLS_MERGE'{
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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}
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withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS'{
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{
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memory = { check_max( 46.GB * task.attempt, 'memory' ) }
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}
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withName: 'GATK4_MARKDUPLICATES'{
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memory = { check_max( 300.GB * task.attempt, 'memory' ) }
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}
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withName: 'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {
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cpus = { check_max( 1 * task.attempt, 'cpus' ) }
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}
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}

‎conf/modules.config‎

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@@ -181,7 +181,7 @@ process {
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}
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withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT' {
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ext.prefix = {"${meta.id}.bed"}
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ext.prefix = {"${meta.id}"}
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publishDir = [
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enabled: params.save_reference,
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mode: params.publish_dir_mode,
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}
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if (params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') {
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if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
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withName: 'NFCORE_SAREK:SAREK:(RECALIBRATE|RECALIBRATE_SPARK):MERGE_INDEX_CRAM:MERGE_CRAM' {
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ext.prefix = { "${meta.id}.recal" }
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ext.when = { meta.num_intervals > 1 }
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]
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}
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if (params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') {
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if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
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withName: 'NFCORE_SAREK:SAREK:CRAM_QC:MOSDEPTH' {
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ext.prefix = { "${meta.id}.recal" }
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}
@@ -794,7 +794,7 @@ process{
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forcegccontentnormalization: params.wes ? "1" : "0",
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minimalsubclonepresence: params.wes ? "30" : "20",
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noisydata: params.wes ? "TRUE" : "FALSE",
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ploidy: params.ploidy,
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ploidy: params.cf_ploidy,
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printNA: params.wes ? "FALSE" : "TRUE",
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readcountthreshold: params.wes ? "50" : "10",
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sex: meta.sex,
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withName: 'FREEC2BED' {
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ext.args = { "${params.ploidy}" }
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ext.args = { "${params.cf_ploidy}" }
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publishDir = [
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mode: params.publish_dir_mode,
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path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
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withName: 'FREEC2CIRCOS' {
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ext.args = { "${params.ploidy}" }
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ext.args = { "${params.cf_ploidy}" }
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publishDir = [
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mode: params.publish_dir_mode,
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path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
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withName: 'MAKEGRAPH' {
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ext.args = { "${params.ploidy}" }
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ext.args = { "${params.cf_ploidy}" }
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publishDir = [
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path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
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"gender": meta.sex,
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"genomeVersion": params.ascat_genome,
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"purity": params.ascat_purity,
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"ploidy": params.ploidy,
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"ploidy": params.ascat_ploidy,
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"minCounts": params.ascat_min_counts,
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"chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')",
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"min_base_qual": params.ascat_min_base_qual,
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forcegccontentnormalization: params.wes ? "1" : "0",
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minimalsubclonepresence: params.wes ? "30" : "20",
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noisydata: params.wes ? "TRUE" : "FALSE",
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ploidy: params.ploidy,
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ploidy: params.cf_ploidy,
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printNA: params.wes ? "FALSE" : "TRUE",
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readcountthreshold: params.wes ? "50" : "10",
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sex: meta.sex,
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if (params.tools && params.tools.split(',').contains('tiddit')) {
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//TIDDIT
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withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
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withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
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ext.prefix = {"${meta.id}.tiddit.normal"}
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}
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withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
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withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
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ext.prefix = {"${meta.id}.tiddit.tumor"}
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}
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//SVDB
1103-
withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' {
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withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_SOMATIC:SVDB_MERGE' {
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ext.prefix = { "${meta.id}.tiddit" }
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publishDir = [
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mode: params.publish_dir_mode,
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path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
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pattern: "*vcf"
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pattern: "*{vcf,vcf.gz}"
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]
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}
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}

‎conf/test.config‎

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}
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function'
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