diff --git a/modules/freebayes/main.nf b/modules/freebayes/main.nf index e67e4c72..73b1da96 100644 --- a/modules/freebayes/main.nf +++ b/modules/freebayes/main.nf @@ -8,10 +8,9 @@ process FREEBAYES { 'quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3' }" input: - tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index) + tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) path fasta path fasta_fai - path targets path samples path populations path cnv @@ -27,7 +26,7 @@ process FREEBAYES { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def input = input_2 ? "${input_1} ${input_2}" : "${input_1}" - def targets_file = targets ? "--target ${targets}" : "" + def targets_file = target_bed ? "--target ${target_bed}" : "" def samples_file = samples ? "--samples ${samples}" : "" def populations_file = populations ? "--populations ${populations}" : "" def cnv_file = cnv ? "--cnv-map ${cnv}" : "" diff --git a/modules/freebayes/meta.yml b/modules/freebayes/meta.yml index abba1daa..e9fb54c2 100644 --- a/modules/freebayes/meta.yml +++ b/modules/freebayes/meta.yml @@ -31,7 +31,11 @@ input: - input_index: type: file description: BAM/CRAM/SAM index file - pattern: "*.bam.bai" + pattern: "*.{bai,crai}" + - target_bed: + type: file + description: Optional - Limit analysis to targets listed in this BED-format FILE. + pattern: "*.bed" - fasta: type: file description: reference fasta file @@ -40,10 +44,6 @@ input: type: file description: reference fasta file index pattern: "*.{fa,fasta}.fai" - - targets: - type: file - description: Optional - Limit analysis to targets listed in this BED-format FILE. - pattern: "*.bed" - samples: type: file description: Optional - Limit analysis to samples listed (one per line) in the FILE. diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 3667a210..6d98874f 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -8,10 +8,12 @@ process GATK4_GETPILEUPSUMMARIES { 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" input: - tuple val(meta), path(bam), path(bai) + tuple val(meta), path(input), path(index), path(intervals) + path fasta + path fai + path dict path variants path variants_tbi - path sites output: tuple val(meta), path('*.pileups.table'), emit: table @@ -23,9 +25,8 @@ process GATK4_GETPILEUPSUMMARIES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sitesCommand = '' - - sitesCommand = sites ? " -L ${sites} " : " -L ${variants} " + def sitesCommand = intervals ? " -L ${intervals} " : " -L ${variants} " + def reference = fasta ? " -R ${fasta}" :"" def avail_mem = 3 if (!task.memory) { @@ -35,9 +36,10 @@ process GATK4_GETPILEUPSUMMARIES { } """ gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\ - -I $bam \\ + -I $input \\ -V $variants \\ $sitesCommand \\ + ${reference} \\ -O ${prefix}.pileups.table \\ $args diff --git a/modules/gatk4/getpileupsummaries/meta.yml b/modules/gatk4/getpileupsummaries/meta.yml index 0add299b..ccf6446d 100644 --- a/modules/gatk4/getpileupsummaries/meta.yml +++ b/modules/gatk4/getpileupsummaries/meta.yml @@ -23,14 +23,30 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test' ] - - bam: + - input: type: file - description: BAM file to be summarised. - pattern: "*.bam" - - bai: + description: BAM/CRAM file to be summarised. + pattern: "*.{bam,cram}" + - input_index: type: file - description: BAM file index. - pattern: "*.bam.bai" + description: BAM/CRAM file index. + pattern: "*.{bai,crai}" + - intervals: + type: file + description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. + pattern: "*.interval_list" + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" - variants: type: file description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified. @@ -39,10 +55,7 @@ input: type: file description: Index file for the germline resource. pattern: "*.vcf.gz.tbi" - - sites: - type: file - description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. - pattern: "*.interval_list" + output: - pileup: diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index 1c8c3993..a7afe86d 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -8,11 +8,10 @@ process GATK4_MUTECT2 { 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" input: - tuple val(meta) , path(input) , path(input_index) , val(which_norm) + tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm) val run_single val run_pon val run_mito - val interval_label path fasta path fai path dict @@ -38,6 +37,7 @@ process GATK4_MUTECT2 { def normals_command = '' def inputs_command = '-I ' + input.join( ' -I ') + def interval = intervals ? "-L ${intervals}" : "" if(run_pon) { panels_command = '' @@ -48,7 +48,7 @@ process GATK4_MUTECT2 { normals_command = '' } else if(run_mito){ - panels_command = "-L ${interval_label} --mitochondria-mode" + panels_command = "-L ${intervals} --mitochondria-mode" normals_command = '' } else { @@ -68,6 +68,7 @@ process GATK4_MUTECT2 { ${inputs_command} \\ ${normals_command} \\ ${panels_command} \\ + ${interval} \\ -O ${prefix}.vcf.gz \\ $args diff --git a/modules/gatk4/mutect2/meta.yml b/modules/gatk4/mutect2/meta.yml index 83f6cb7c..94ce72ee 100644 --- a/modules/gatk4/mutect2/meta.yml +++ b/modules/gatk4/mutect2/meta.yml @@ -30,6 +30,10 @@ input: type: list description: list of BAM file indexes, also able to take CRAM indexes as an input pattern: "*.{bam.bai/cram.crai}" + - intervals: + type: File/string + description: Specify region the tools is run on. + pattern: ".{bed,interval_list}/chrM" - which_norm: type: list description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode) @@ -46,10 +50,6 @@ input: type: boolean description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode pattern: "true/false" - - interval_label: - type: string - description: Specify the label used for mitochondrial chromosome when mutect2 is run in mitochondria mode. - pattern: "chrM" - fasta: type: file description: The reference fasta file diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf index 1ce0da31..3f47d86f 100644 --- a/modules/strelka/germline/main.nf +++ b/modules/strelka/germline/main.nf @@ -8,11 +8,9 @@ process STRELKA_GERMLINE { 'quay.io/biocontainers/strelka:2.9.10--0' }" input: - tuple val(meta), path(input), path(input_index) + tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) path fasta path fai - path target_bed - path target_bed_tbi output: tuple val(meta), path("*variants.vcf.gz") , emit: vcf @@ -27,7 +25,7 @@ process STRELKA_GERMLINE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def regions = target_bed ? "--exome --callRegions ${target_bed}" : "" + def regions = target_bed ? "--callRegions ${target_bed}" : "" """ configureStrelkaGermlineWorkflow.py \\ --bam $input \\ diff --git a/modules/strelka/somatic/main.nf b/modules/strelka/somatic/main.nf index 22cce8cb..b61c09bd 100644 --- a/modules/strelka/somatic/main.nf +++ b/modules/strelka/somatic/main.nf @@ -8,11 +8,9 @@ process STRELKA_SOMATIC { 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" input: - tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi) + tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) path fasta path fai - path target_bed - path target_bed_tbi output: tuple val(meta), path("*.somatic_indels.vcf.gz") , emit: vcf_indels @@ -27,15 +25,16 @@ process STRELKA_SOMATIC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : "" + def options_target_bed = target_bed ? "--callRegions ${target_bed}" : "" def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : "" """ + configureStrelkaSomaticWorkflow.py \\ --tumor $input_tumor \\ --normal $input_normal \\ --referenceFasta $fasta \\ - $options_target_bed \\ - $options_manta \\ + ${options_target_bed} \\ + ${options_manta} \\ $args \\ --runDir strelka diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 3f42ad21..12657599 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -22,7 +22,7 @@ process TABIX_BGZIPTABIX { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - bgzip -c $args $input > ${prefix}.gz + bgzip --threads ${task.cpus} -c $args $input > ${prefix}.gz tabix $args2 ${prefix}.gz cat <<-END_VERSIONS > versions.yml diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 7d0d3efa..165e8449 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -122,6 +122,9 @@ params { genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" + genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" + genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" @@ -262,6 +265,9 @@ params { test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" + test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" + test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" diff --git a/tests/modules/freebayes/main.nf b/tests/modules/freebayes/main.nf index f8ae0ecb..6ed708c5 100644 --- a/tests/modules/freebayes/main.nf +++ b/tests/modules/freebayes/main.nf @@ -5,91 +5,98 @@ nextflow.enable.dsl = 2 include { FREEBAYES } from '../../../modules/freebayes/main.nf' workflow test_freebayes { - + targets = [] input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), [], - [] + [], + targets ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = [] + samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_bed { + targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), [], - [] + [], + targets ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_cram { + targets = [] input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], - [] + [], + targets ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = [] samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_somatic { + targets = [] input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + targets ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = [] + samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_somatic_cram_intervals { + targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true), + targets ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } diff --git a/tests/modules/freebayes/test.yml b/tests/modules/freebayes/test.yml index 6cca692e..c3c8e30b 100644 --- a/tests/modules/freebayes/test.yml +++ b/tests/modules/freebayes/test.yml @@ -4,7 +4,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 81d3e6ce7b6343d088b779567c3803eb + md5sum: f28d0b8e2ccedeac0e590ca2ecaac83d - path: output/freebayes/versions.yml md5sum: 53651eb835af65df829241257584a7d2 @@ -14,7 +14,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 02645d014a63485162a7789007373b2a + md5sum: 1927441d1b7a4c48cbb61821de300ad4 - path: output/freebayes/versions.yml md5sum: becc93c8a0be580c09d55b955d60a5e1 @@ -24,7 +24,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 3d0bfcd2129c62f8863952fa4c1054db + md5sum: 9b8d1d51d779bbea4086c7f7a2ece641 - path: output/freebayes/versions.yml md5sum: 2e5b266edfc6cab81353cfc72c00f67c @@ -34,7 +34,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 22fec868210ba3baf685b214bfd8e74b + md5sum: dcaa639912174055c1380913d6102c01 - path: output/freebayes/versions.yml md5sum: 8fbdb4c052fb3e42b5508a966125fa05 @@ -44,6 +44,6 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 527cf2937067bbd4117d95fd472bb928 + md5sum: b0052a2b83c0ba1b9686d0c96e61712f - path: output/freebayes/versions.yml md5sum: af97e3dfdc086188739907c3460e49e0 diff --git a/tests/modules/gatk4/getpileupsummaries/main.nf b/tests/modules/gatk4/getpileupsummaries/main.nf index 54a9b1f5..b0de9d6e 100644 --- a/tests/modules/gatk4/getpileupsummaries/main.nf +++ b/tests/modules/gatk4/getpileupsummaries/main.nf @@ -8,24 +8,45 @@ workflow test_gatk4_getpileupsummaries_just_variants { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ] + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + [] + ] variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) - sites = [] - - GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites ) + fasta = [] + fai = [] + dict = [] + GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi ) } workflow test_gatk4_getpileupsummaries_separate_sites { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ] + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) ] variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) - sites = file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) - - GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites ) + fasta = [] + fai = [] + dict = [] + GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi) +} + +workflow test_gatk4_getpileupsummaries_separate_sites_cram { + + input = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) , + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + ] + + variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi) } diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml index 65ea30e7..c032acf0 100644 --- a/tests/modules/gatk4/getpileupsummaries/test.yml +++ b/tests/modules/gatk4/getpileupsummaries/test.yml @@ -1,17 +1,32 @@ - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants - command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config + command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config tags: - - gatk4 - gatk4/getpileupsummaries + - gatk4 files: - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 + - path: output/gatk4/versions.yml + md5sum: dd98374e3b5d35ddd1c6b3fa7e662dc5 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites - command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config + command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config tags: - - gatk4 - gatk4/getpileupsummaries + - gatk4 files: - - path: output/gatk4/test.pileups.table + - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 + - path: output/gatk4/versions.yml + md5sum: 080b6af7df182558aeab117668388d59 + +- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram + command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config + tags: + - gatk4/getpileupsummaries + - gatk4 + files: + - path: output/gatk4/test.pileups.table + md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 + - path: output/gatk4/versions.yml + md5sum: 33458a9efa6d61c713af9f7b722d7134 diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf index 94cf0416..19b22914 100644 --- a/tests/modules/gatk4/mutect2/main.nf +++ b/tests/modules/gatk4/mutect2/main.nf @@ -12,12 +12,12 @@ workflow test_gatk4_mutect2_tumor_normal_pair { [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ], + [], ["normal"] ] run_single = false run_pon = false run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -26,19 +26,19 @@ workflow test_gatk4_mutect2_tumor_normal_pair { panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } workflow test_gatk4_mutect2_tumor_single { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [], [] ] run_single = true run_pon = false run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -47,19 +47,19 @@ workflow test_gatk4_mutect2_tumor_single { panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } workflow test_gatk4_mutect2_cram_input { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)], + [], [] ] run_single = true run_pon = false run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -68,19 +68,19 @@ workflow test_gatk4_mutect2_cram_input { panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } workflow test_gatk4_mutect2_generate_pon { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [], [] ] run_single = false run_pon = true run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -89,7 +89,7 @@ workflow test_gatk4_mutect2_generate_pon { panel_of_normals = [] panel_of_normals_tbi = [] - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } // mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working. @@ -97,12 +97,12 @@ workflow test_gatk4_mutect2_mitochondria { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)], [] ] run_single = false run_pon = false run_mito = true - interval_label = 'chr22' fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) @@ -111,5 +111,5 @@ workflow test_gatk4_mutect2_mitochondria { panel_of_normals = [] panel_of_normals_tbi = [] - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } diff --git a/tests/modules/gatk4/mutect2/nextflow.config b/tests/modules/gatk4/mutect2/nextflow.config index 0966fc15..8730f1c4 100644 --- a/tests/modules/gatk4/mutect2/nextflow.config +++ b/tests/modules/gatk4/mutect2/nextflow.config @@ -2,8 +2,4 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_TEMPFIX_MUTECT2 { - ext.args = '--mitochondria-mode' - } - } diff --git a/tests/modules/strelka/germline/main.nf b/tests/modules/strelka/germline/main.nf index c50d76e1..312a4f72 100644 --- a/tests/modules/strelka/germline/main.nf +++ b/tests/modules/strelka/germline/main.nf @@ -9,28 +9,29 @@ workflow test_strelka_germline { [ id:'test'], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + [], + [] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - target_bed = [] - target_bed_tbi = [] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi ) + STRELKA_GERMLINE ( input, fasta, fai) } workflow test_strelka_germline_target_bed { + input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - target_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi ) + STRELKA_GERMLINE ( input, fasta, fai) } diff --git a/tests/modules/strelka/germline/nextflow.config b/tests/modules/strelka/germline/nextflow.config index 8730f1c4..5983e1b8 100644 --- a/tests/modules/strelka/germline/nextflow.config +++ b/tests/modules/strelka/germline/nextflow.config @@ -1,5 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - + withName: STRELKA_GERMLINE { + ext.args = '--exome' + } } diff --git a/tests/modules/strelka/somatic/main.nf b/tests/modules/strelka/somatic/main.nf index b1d4efeb..ab75f0e2 100644 --- a/tests/modules/strelka/somatic/main.nf +++ b/tests/modules/strelka/somatic/main.nf @@ -12,18 +12,19 @@ workflow test_strelka_somatic { file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), - [],[] + [],[], + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_SOMATIC (input, fasta, fai, bed, bed_tbi ) + STRELKA_SOMATIC (input, fasta, fai ) } -workflow test_strelka__best_practices_somatic { +workflow test_strelka_best_practices_somatic { + input = [ [ id:'test', single_end:false ], // meta map @@ -31,14 +32,14 @@ workflow test_strelka__best_practices_somatic { file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_SOMATIC ( input, fasta, fai, bed, bed_tbi ) + STRELKA_SOMATIC ( input, fasta, fai ) } diff --git a/tests/modules/strelka/somatic/nextflow.config b/tests/modules/strelka/somatic/nextflow.config index 8730f1c4..5676ba15 100644 --- a/tests/modules/strelka/somatic/nextflow.config +++ b/tests/modules/strelka/somatic/nextflow.config @@ -1,5 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - + withName: STRELKA_SOMATIC { + ext.args = '--exome' + } } diff --git a/tests/modules/strelka/somatic/test.yml b/tests/modules/strelka/somatic/test.yml index a56f955a..787f3b19 100644 --- a/tests/modules/strelka/somatic/test.yml +++ b/tests/modules/strelka/somatic/test.yml @@ -6,20 +6,16 @@ files: - path: output/strelka/test.somatic_indels.vcf.gz - path: output/strelka/test.somatic_indels.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - path: output/strelka/test.somatic_snvs.vcf.gz - path: output/strelka/test.somatic_snvs.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 -- name: strelka somatic test_strelka__best_practices_somatic - command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka__best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config +- name: strelka somatic test_strelka_best_practices_somatic + command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config tags: - strelka - strelka/somatic files: - path: output/strelka/test.somatic_indels.vcf.gz - path: output/strelka/test.somatic_indels.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - path: output/strelka/test.somatic_snvs.vcf.gz - path: output/strelka/test.somatic_snvs.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905