diff --git a/CHANGELOG.md b/CHANGELOG.md index e8abf029be..a1974ca388 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -49,6 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#957](https://github.com/nf-core/sarek/pull/957) - Add `failOnDuplicate` and `failOnMismatch` options to all `join()` operator where it was possible - [#982](https://github.com/nf-core/sarek/pull/982) - Remove usage of exit statements, using `Nextflow.error` instead - [#985](https://github.com/nf-core/sarek/pull/985) - Cache correctly identifies when it needs to be updated +- [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility ### Deprecated diff --git a/conf/modules/ascat.config b/conf/modules/ascat.config index 9ee66663a0..8a8cf79999 100644 --- a/conf/modules/ascat.config +++ b/conf/modules/ascat.config @@ -22,7 +22,7 @@ process { "purity": params.ascat_purity, "ploidy": params.ascat_ploidy, "minCounts": params.ascat_min_counts, - "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')", + "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')", // for faster testing use "c('21', '22')" "min_base_qual": params.ascat_min_base_qual, "min_map_qual": params.ascat_min_map_qual ]} diff --git a/conf/test/test_tools_somatic_ascat.config b/conf/test/test_tools_somatic_ascat.config index 274e8ee83e..3f37bd4b3f 100644 --- a/conf/test/test_tools_somatic_ascat.config +++ b/conf/test/test_tools_somatic_ascat.config @@ -13,13 +13,11 @@ params { input = "${projectDir}/tests/csv/3.0/ascat_somatic.csv" genome = 'GATK.GRCh37' igenomes_ignore = false - ascat_chromosomes = 'c("21", "22")' - ascat_loci = "/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip" + ascat_loci = "G1000_loci_hg19.zip" ascat_min_base_qual = 30 chr_dir = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'] germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'] intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'] - joint_germline = true step = 'variant_calling' tools = 'ascat' wes = false diff --git a/modules.json b/modules.json index d2a1641a00..fc38461b19 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "ascat": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "1fda5ab75106682f329bde25d4226640d353c3d7", "installed_by": ["modules"] }, "bcftools/concat": { diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf index 88ee819d14..de9a555db0 100644 --- a/modules/nf-core/ascat/main.nf +++ b/modules/nf-core/ascat/main.nf @@ -2,10 +2,10 @@ process ASCAT { tag "$meta.id" label 'process_medium' - conda "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" + conda "bioconda::ascat=3.1.1 bioconda::cancerit-allelecount=4.3.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0': - 'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:ba3e6d2157eac2d38d22e62ec87675e12adb1010-0': + 'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:ba3e6d2157eac2d38d22e62ec87675e12adb1010-0' }" input: tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor) @@ -81,7 +81,8 @@ process ASCAT { $min_map_qual_arg $fasta_arg $skip_allele_counting_tumour_arg - $skip_allele_counting_normal_arg + $skip_allele_counting_normal_arg, + seed = 42 ) @@ -116,7 +117,7 @@ process ASCAT { } #Segment the data - ascat.bc = ascat.aspcf(ascat.bc) + ascat.bc = ascat.aspcf(ascat.bc, seed=42) #Plot the segmented data ascat.plotSegmentedData(ascat.bc) diff --git a/modules/nf-core/ascat/meta.yml b/modules/nf-core/ascat/meta.yml index 0a24567f91..104ef0fb33 100644 --- a/modules/nf-core/ascat/meta.yml +++ b/modules/nf-core/ascat/meta.yml @@ -7,7 +7,7 @@ keywords: tools: - ascat: description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). - homepage: None + documentation: https://github.com/VanLoo-lab/ascat/tree/master/man tool_dev_url: https://github.com/VanLoo-lab/ascat doi: "10.1093/bioinformatics/btaa538" diff --git a/tests/csv/3.0/ascat_somatic.csv b/tests/csv/3.0/ascat_somatic.csv index b7484f28b6..8eb30f5531 100644 --- a/tests/csv/3.0/ascat_somatic.csv +++ b/tests/csv/3.0/ascat_somatic.csv @@ -1,3 +1,3 @@ patient,sex,status,sample,cram,crai -test3,XX,0,sample3,/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,/mnt/volume/ascat/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai -test3,XX,1,sample4,/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,/mnt/volume/ascat/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai +test3,XX,0,sample3,HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai +test3,XX,1,sample4,HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram,HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index d64794170a..955cd0836a 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -6,34 +6,34 @@ - somatic - variant_calling files: - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png - md5sum: 4ac774bf5f1157e77426fd82f5a03001 + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalBAF.txt + md5sum: b73a38fd183143b1e8aed9f261a9c5f0 + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt + md5sum: 29f29092c19274aa3d5fd4f9e3828cbb - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.tumour.png - md5sum: 4ac774bf5f1157e77426fd82f5a03002 - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png - md5sum: 4ac774bf5f1157e77426fd82f5a03003 + md5sum: df246ef9c2c4dc868901afe17366e116 - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.tumour.png - md5sum: 4ac774bf5f1157e77426fd82f5a03004 + md5sum: 7629826e2e02ab99bedbab75b0c022a5 - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.cnvs.txt - md5sum: 1ade39990eda42baaedfd1c041070cd5 + md5sum: 68b329da9893e34099c7d8ad5cb9c940 + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt + md5sum: 5235f69624ab91f395ebf30b90c02e9e + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.ASPCF.png + md5sum: 883075c53513dea8bbcb85ad564cb641 + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png + md5sum: 1a47cc241548fa89f914c2f5bfee6bee - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.metrics.txt - md5sum: 6257cd36d411ea16c577ca3a594feb03 + md5sum: f7e486e5eed6166dedf9306235f537ec + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png + md5sum: 1a47cc241548fa89f914c2f5bfee6bee - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.purityploidy.txt - md5sum: e888f26ac0474bd69de2f39cbfe71956 + md5sum: f1484c2b120834d3db8774ad02a038b9 + - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.sunrise.png + md5sum: a2bf4b04176983a87b85843c789eaab8 - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.segments.txt - md5sum: 73469d4382fc72b6c1d11f3491ef6654 - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.ASPCF.png - md5sum: 4ac774bf5f1157e77426fd82f5a03009 - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalBAF.txt - md5sum: 4ac774bf5f1157e77426fd82f5a03010 + md5sum: 68b329da9893e34099c7d8ad5cb9c940 - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt - md5sum: cbb7adfd1780fd98c5231cdc48121d78 - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour.sunrise.png - md5sum: 4ac774bf5f1157e77426fd82f5a03012 - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourBAF.txt - md5sum: 4ac774bf5f1157e77426fd82f5a03013 - - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt - md5sum: c6ef56244b8ac53d2c949437918523b2 + md5sum: 05418a7d814db11808172a4f57d040a1 - name: Run variant calling on somatic sample with mutect2 without intervals command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --no_intervals --outdir results tags: