diff --git a/README.md b/README.md index 6a63a30eb..17d2271ba 100644 --- a/README.md +++ b/README.md @@ -17,8 +17,27 @@ graph TD B --> D[CONCAT_CHUNKED_VCFS] B --> F[EXTRACT_SAMPLE_IDS] F --> G[GENERATE_PHENO_COV] + H[results/chunked_vcfs] --> I[FIXTURE_SELECT_SAMPLES] + H --> J[FIXTURE_THIN_CHROMOSOME] + I --> J + J --> K[FIXTURE_MERGE_CHROMOSOMES] + K --> L[FIXTURE_PCA] + K --> M[FIXTURE_CAUSAL_WEIGHTS] + M --> N[FIXTURE_SCORE_LIABILITY] + K --> N + L --> O[FIXTURE_PHENO_COVAR] + N --> O + I --> O + J --> P[FIXTURE_EXPORT_FORMATS] + K --> P + P --> Q[FIXTURE_COMPRESS_VCF] ``` +The two stages are independent. The upper stage downloads the 1000 Genomes release +and chunks it; its output is already committed, so it is skipped with +`--skip_source_generation`. The lower stage derives the GWAS pipeline fixtures from +that committed output and never touches the network. + ## Git clone the gwas pipeline test data If you want to get a local copy of the test data, you can either git clone the whole test data material, including all test data for all nf-core pipelnies, or if you want to save storage space you can clone the example data for one specific pipeline. @@ -60,11 +79,30 @@ results/ ├── pheno_cov/ │   ├── example.pheno │   └── example.covar +├── fixtures/ +│ ├── README.md +│ ├── genotypes/ +│ │ ├── example_chr1.{pgen,pvar,psam,bed,bim,fam,vcf.gz,vcf.gz.tbi} +│ │ ├── example_chr2.{...} +│ │ ├── ... (one bundle per autosome, chr1..chr22) +│ │ ├── example_chr22.{...} +│ │ └── example_all.{...} +│ └── pheno_cov/ +│ ├── example.pheno +│ ├── example.covar +│ ├── example.qcovar +│ ├── example.catcovar +│ ├── causal_weights.tsv +│ ├── fixture_samples.tsv +│ ├── fixture_sex.tsv +│ └── fixture_summary.txt ``` Each chromosome-specific VCF file (chr\*.vcf.gz) is accompanied by its corresponding tabix index (.vcf.gz.tbi), enabling efficient querying. A combined VCF and index are also included for downstream association tests or visualization. +`results/fixtures/` holds the pipeline-level GWAS fixtures: 500 samples across all 22 autosomes, 4942 LD-thinned variants (`--indep-pairwise 100 10 0.2`), the same samples and variants in PLINK 2, PLINK 1 and VCF encodings, a headered phenotype file with a simulated signal-bearing quantitative trait and a simulated binary trait, and headered covariate files carrying sex, age and principal components. They are derived from `results/chunked_vcfs/` with no download step. See [`results/fixtures/README.md`](results/fixtures/README.md) for the dimensions, how the traits were simulated, and how to regenerate them. + ## Support For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging). diff --git a/main.nf b/main.nf index 9bbdaf480..9f0435972 100644 --- a/main.nf +++ b/main.nf @@ -7,23 +7,87 @@ include { CONCAT_CHUNKED_VCFS } from './modules/concat_chunked_vcfs.nf' include { EXTRACT_SAMPLE_IDS } from './modules/extract_sample_ids.nf' include { GENERATE_PHENO_COV } from './modules/generate_pheno_cov.nf' include { INDEX_CHUNKED_VCFS } from './modules/index_chunked_vcfs.nf' +include { FIXTURE_SELECT_SAMPLES } from './modules/fixture_select_samples.nf' +include { FIXTURE_THIN_CHROMOSOME } from './modules/fixture_thin_chromosome.nf' +include { FIXTURE_MERGE_CHROMOSOMES } from './modules/fixture_merge_chromosomes.nf' +include { FIXTURE_PCA } from './modules/fixture_pca.nf' +include { FIXTURE_CAUSAL_WEIGHTS } from './modules/fixture_causal_weights.nf' +include { FIXTURE_SCORE_LIABILITY } from './modules/fixture_score_liability.nf' +include { FIXTURE_PHENO_COVAR } from './modules/fixture_pheno_covar.nf' +include { FIXTURE_EXPORT_FORMATS } from './modules/fixture_export_formats.nf' +include { FIXTURE_COMPRESS_VCF } from './modules/fixture_compress_vcf.nf' workflow { - // Run the download process - GENERATE_EXAMPLE_GENOTYPES_VCFS() - - def vcfs_with_chr = GENERATE_EXAMPLE_GENOTYPES_VCFS.out.vcfs - .flatten() - .map { file -> - def chr = file.name.toString().split("\\.")[1] // safer than `tokenize` - tuple(chr, file) - } - - // Feed the tuples into the chunking process - CHUNK_VCFS(vcfs_with_chr) - chr1_chunked = CHUNK_VCFS.out.chunked_vcfs.filter { chr, file -> chr == 'chr1'}.map { chr, file -> file } - EXTRACT_SAMPLE_IDS(chr1_chunked) - GENERATE_PHENO_COV(EXTRACT_SAMPLE_IDS.out.sample_ids) - INDEX_CHUNKED_VCFS(CHUNK_VCFS.out.chunked_vcfs) - all_chunked_vcfs = CHUNK_VCFS.out.chunked_vcfs.map { chr, file -> file }.collect() - CONCAT_CHUNKED_VCFS(all_chunked_vcfs) + // Source-data stage: download the 1000 Genomes release and chunk it. Skipped + // with --skip_source_generation, because its output is already committed under + // results/chunked_vcfs and re-running it re-downloads tens of gigabytes. + if (!params.skip_source_generation) { + // Run the download process + GENERATE_EXAMPLE_GENOTYPES_VCFS() + + def vcfs_with_chr = GENERATE_EXAMPLE_GENOTYPES_VCFS.out.vcfs + .flatten() + .map { file -> + def chr = file.name.toString().split("\\.")[1] // safer than `tokenize` + tuple(chr, file) + } + + // Feed the tuples into the chunking process + CHUNK_VCFS(vcfs_with_chr) + chr1_chunked = CHUNK_VCFS.out.chunked_vcfs.filter { chr, file -> chr == 'chr1'}.map { chr, file -> file } + EXTRACT_SAMPLE_IDS(chr1_chunked) + GENERATE_PHENO_COV(EXTRACT_SAMPLE_IDS.out.sample_ids) + INDEX_CHUNKED_VCFS(CHUNK_VCFS.out.chunked_vcfs) + all_chunked_vcfs = CHUNK_VCFS.out.chunked_vcfs.map { chr, file -> file }.collect() + CONCAT_CHUNKED_VCFS(all_chunked_vcfs) + } + + // GWAS fixture stage: derive the pipeline-level test fixtures from the + // already-committed chromosome-chunked VCFs. Nothing here reads the network. + def fixture_chrs = params.fixture_chromosomes.tokenize(',').collect { chr -> chr.trim() } + def fixture_sources = channel + .fromList(fixture_chrs) + .map { chr -> tuple(chr, file("${params.chunked_vcfs_dir}/${chr}_chunked.vcf.gz", checkIfExists: true)) } + + // The sample subset is taken from the first fixture chromosome; every chunked + // VCF carries the same 2504 samples in the same order. + FIXTURE_SELECT_SAMPLES( + file("${params.chunked_vcfs_dir}/${fixture_chrs.first()}_chunked.vcf.gz", checkIfExists: true) + ) + + FIXTURE_THIN_CHROMOSOME( + fixture_sources, + FIXTURE_SELECT_SAMPLES.out.samples, + FIXTURE_SELECT_SAMPLES.out.sex + ) + + FIXTURE_MERGE_CHROMOSOMES( + fixture_chrs, + FIXTURE_THIN_CHROMOSOME.out.pgen + .map { prefix, pgen, pvar, psam -> [pgen, pvar, psam] } + .collect() + ) + + FIXTURE_PCA(FIXTURE_MERGE_CHROMOSOMES.out.pgen) + + FIXTURE_CAUSAL_WEIGHTS( + FIXTURE_MERGE_CHROMOSOMES.out.pgen.map { prefix, pgen, pvar, psam -> pvar } + ) + + FIXTURE_SCORE_LIABILITY( + FIXTURE_MERGE_CHROMOSOMES.out.pgen, + FIXTURE_CAUSAL_WEIGHTS.out.weights + ) + + FIXTURE_PHENO_COVAR( + FIXTURE_SCORE_LIABILITY.out.sscore, + FIXTURE_PCA.out.eigenvec, + FIXTURE_SELECT_SAMPLES.out.sex + ) + + // Per-chromosome and combined bundles are both emitted: leave-one-chromosome-out + // methods need the per-chromosome split, single-cohort methods want the merge. + def fixture_bundles = FIXTURE_THIN_CHROMOSOME.out.pgen.mix(FIXTURE_MERGE_CHROMOSOMES.out.pgen) + + FIXTURE_EXPORT_FORMATS(fixture_bundles) + FIXTURE_COMPRESS_VCF(FIXTURE_EXPORT_FORMATS.out.vcf) } diff --git a/modules/extract_sample_ids.nf b/modules/extract_sample_ids.nf index c66a60509..e50841e78 100644 --- a/modules/extract_sample_ids.nf +++ b/modules/extract_sample_ids.nf @@ -1,6 +1,6 @@ process EXTRACT_SAMPLE_IDS { container "community.wave.seqera.io/library/r-base:4.4.3--1e564c44feffeaa0" - publishDir params.outdir_pheno_cov, mode: 'symlink' + publishDir params.outdir_pheno_cov, mode: 'copy' input: path vcf_file diff --git a/modules/fixture_causal_weights.nf b/modules/fixture_causal_weights.nf new file mode 100644 index 000000000..9a87dfa48 --- /dev/null +++ b/modules/fixture_causal_weights.nf @@ -0,0 +1,55 @@ +// Draw the causal variants and their effect sizes for the simulated traits. +// +// Two disjoint causal sets are drawn from the merged fixture variants, one for the +// quantitative trait and one for the binary trait's genetic liability, so the two +// traits are not collinear. Every draw goes through a fixed seed with the RNG kind +// pinned explicitly, so the weight file is byte-identical on every run. +process FIXTURE_CAUSAL_WEIGHTS { + container "community.wave.seqera.io/library/r-base:4.4.3--1e564c44feffeaa0" + publishDir params.outdir_fixture_pheno_cov, mode: 'copy' + + input: + path pvar + + output: + path "causal_weights.tsv", emit: weights + + script: + """ + #!/usr/bin/env Rscript + set.seed(${params.fixture_seed}, + kind = "Mersenne-Twister", + normal.kind = "Inversion", + sample.kind = "Rejection") + + variants <- read.table("${pvar}", comment.char = "#", header = FALSE, + stringsAsFactors = FALSE) + colnames(variants) <- c("CHROM", "POS", "ID", "REF", "ALT") + n_variants <- nrow(variants) + + n_causal <- ${params.fixture_n_causal} + if (2 * n_causal > n_variants) { + stop("not enough variants for two disjoint causal sets") + } + + drawn <- sample.int(n_variants, 2 * n_causal) + causal_qt <- sort(drawn[seq_len(n_causal)]) + causal_bt <- sort(drawn[n_causal + seq_len(n_causal)]) + + weights <- data.frame(ID = variants[["ID"]], + A1 = variants[["ALT"]], + BETA_QT = 0, + BETA_BT = 0, + stringsAsFactors = FALSE) + weights[["BETA_QT"]][causal_qt] <- round(rnorm(n_causal), 6) + weights[["BETA_BT"]][causal_bt] <- round(rnorm(n_causal), 6) + + write.table(weights, file = "causal_weights.tsv", sep = "\\t", quote = FALSE, + row.names = FALSE, col.names = TRUE) + """ + + stub: + """ + printf 'ID\\tA1\\tBETA_QT\\tBETA_BT\\n' > causal_weights.tsv + """ +} diff --git a/modules/fixture_compress_vcf.nf b/modules/fixture_compress_vcf.nf new file mode 100644 index 000000000..7f494d0c8 --- /dev/null +++ b/modules/fixture_compress_vcf.nf @@ -0,0 +1,27 @@ +// Block-compress and index the exported fixture VCFs. +// +// The ##fileDate header line plink2 writes carries the run date, which would make +// the committed fixture differ on every regeneration; it is dropped so the VCF is +// byte-reproducible. +process FIXTURE_COMPRESS_VCF { + container "community.wave.seqera.io/library/bcftools_tabix_pip_tools:48085064a9189d8c" + publishDir params.outdir_fixture_genotypes, mode: 'copy' + + input: + tuple val(prefix), path(vcf_file) + + output: + tuple val(prefix), path("${prefix}.vcf.gz"), path("${prefix}.vcf.gz.tbi"), emit: vcf + + script: + """ + grep -v '^##fileDate=' ${vcf_file} | bgzip -c > ${prefix}.vcf.gz + tabix -p vcf ${prefix}.vcf.gz + """ + + stub: + """ + printf '##fileformat=VCFv4.3\\n#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\tFORMAT\\n' | bgzip -c > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + """ +} diff --git a/modules/fixture_export_formats.nf b/modules/fixture_export_formats.nf new file mode 100644 index 000000000..10e0a81fc --- /dev/null +++ b/modules/fixture_export_formats.nf @@ -0,0 +1,36 @@ +// Re-encode a PLINK 2 fixture bundle as PLINK 1 binary and as VCF, so all three +// encodings describe exactly the same samples and variants. +process FIXTURE_EXPORT_FORMATS { + container "community.wave.seqera.io/library/plink2:2.0.0a.6.9--e6710830a4b7f0c6" + publishDir params.outdir_fixture_genotypes, mode: 'copy', pattern: "*.{bed,bim,fam}" + + input: + tuple val(prefix), path(pgen), path(pvar), path(psam) + + output: + tuple val(prefix), path("${prefix}.bed"), path("${prefix}.bim"), path("${prefix}.fam"), emit: bed + tuple val(prefix), path("${prefix}.vcf"), emit: vcf + + script: + """ + plink2 \\ + --pfile ${prefix} \\ + --threads 1 \\ + --seed 1 \\ + --make-bed \\ + --out ${prefix} + + plink2 \\ + --pfile ${prefix} \\ + --threads 1 \\ + --seed 1 \\ + --export vcf id-paste=iid \\ + --out ${prefix} + """ + + stub: + """ + touch ${prefix}.bed ${prefix}.bim ${prefix}.fam + printf '##fileformat=VCFv4.3\\n#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\tFORMAT\\n' > ${prefix}.vcf + """ +} diff --git a/modules/fixture_merge_chromosomes.nf b/modules/fixture_merge_chromosomes.nf new file mode 100644 index 000000000..9f77de9b7 --- /dev/null +++ b/modules/fixture_merge_chromosomes.nf @@ -0,0 +1,36 @@ +// Merge the per-chromosome PLINK 2 fixtures into one multi-chromosome bundle. +// +// The merge list is built from the ordered chromosome list rather than from the +// staged file order, so the merged variant order is reproducible. +process FIXTURE_MERGE_CHROMOSOMES { + container "community.wave.seqera.io/library/plink2:2.0.0a.6.9--e6710830a4b7f0c6" + publishDir params.outdir_fixture_genotypes, mode: 'copy', pattern: "*.{pgen,pvar,psam}" + + input: + val chrs + path psets + + output: + tuple val("${params.fixture_prefix}_all"), path("${params.fixture_prefix}_all.pgen"), path("${params.fixture_prefix}_all.pvar"), path("${params.fixture_prefix}_all.psam"), emit: pgen + + script: + def prefix = "${params.fixture_prefix}_all" + def merge_list = chrs.collect { chr -> "${params.fixture_prefix}_${chr}" }.join('\\n') + """ + printf '${merge_list}\\n' > merge_list.txt + + plink2 \\ + --pmerge-list merge_list.txt pfile \\ + --threads 1 \\ + --seed 1 \\ + --out ${prefix} + """ + + stub: + def prefix = "${params.fixture_prefix}_all" + """ + touch ${prefix}.pgen + printf '#CHROM\\tPOS\\tID\\tREF\\tALT\\n' > ${prefix}.pvar + printf '#FID\\tIID\\tSEX\\n' > ${prefix}.psam + """ +} diff --git a/modules/fixture_pca.nf b/modules/fixture_pca.nf new file mode 100644 index 000000000..f861a37bc --- /dev/null +++ b/modules/fixture_pca.nf @@ -0,0 +1,29 @@ +// Principal components of the merged fixture genotypes, used as covariates. +// Exact (non-approximate) PCA, so the result is a deterministic function of the +// genotype matrix. +process FIXTURE_PCA { + container "community.wave.seqera.io/library/plink2:2.0.0a.6.9--e6710830a4b7f0c6" + + input: + tuple val(prefix), path(pgen), path(pvar), path(psam) + + output: + path "${prefix}.eigenvec", emit: eigenvec + path "${prefix}.eigenval", emit: eigenval + + script: + """ + plink2 \\ + --pfile ${prefix} \\ + --pca ${params.fixture_n_pcs_computed} \\ + --threads 1 \\ + --seed 1 \\ + --out ${prefix} + """ + + stub: + """ + printf '#FID\\tIID\\tPC1\\n' > ${prefix}.eigenvec + printf '0.0\\n' > ${prefix}.eigenval + """ +} diff --git a/modules/fixture_pheno_covar.nf b/modules/fixture_pheno_covar.nf new file mode 100644 index 000000000..23b973dfb --- /dev/null +++ b/modules/fixture_pheno_covar.nf @@ -0,0 +1,131 @@ +// Assemble the headered phenotype and covariate fixtures from the genotype-derived +// scores, the genotype-derived principal components and the deterministic sex +// assignment. +// +// The quantitative trait and the binary trait's liability are built as +// sqrt(h2) * standardised genetic score +// + sqrt(c2) * standardised covariate effect +// + sqrt(1 - h2 - c2) * noise +// so both traits carry real genetic signal from the fixture genotypes and both +// respond to the supplied covariates. The binary trait is the liability +// dichotomised at the exact empirical quantile matching the target prevalence, so +// the case count is fixed rather than sampled. +process FIXTURE_PHENO_COVAR { + container "community.wave.seqera.io/library/r-base:4.4.3--1e564c44feffeaa0" + publishDir params.outdir_fixture_pheno_cov, mode: 'copy' + + input: + path sscore + path eigenvec + path sex + + output: + path "${params.fixture_prefix}.pheno", emit: pheno + path "${params.fixture_prefix}.covar", emit: covar + path "${params.fixture_prefix}.qcovar", emit: qcovar + path "${params.fixture_prefix}.catcovar", emit: catcovar + path "fixture_summary.txt", emit: summary + + script: + """ + #!/usr/bin/env Rscript + set.seed(${params.fixture_seed}, + kind = "Mersenne-Twister", + normal.kind = "Inversion", + sample.kind = "Rejection") + + read_headed <- function(path) { + frame <- read.delim(path, header = TRUE, check.names = FALSE, + comment.char = "", stringsAsFactors = FALSE) + colnames(frame)[1] <- sub("^#", "", colnames(frame)[1]) + frame + } + + standardise <- function(x) (x - mean(x)) / sd(x) + + scores <- read_headed("${sscore}") + pcs <- read_headed("${eigenvec}") + sexes <- read_headed("${sex}") + + ids <- scores[["IID"]] + n <- length(ids) + pcs <- pcs[match(ids, pcs[["IID"]]), , drop = FALSE] + sexes <- sexes[match(ids, sexes[["IID"]]), , drop = FALSE] + stopifnot(!anyNA(pcs[["IID"]]), !anyNA(sexes[["IID"]])) + + h2 <- ${params.fixture_h2} + c2 <- ${params.fixture_covariate_variance} + e2 <- 1 - h2 - c2 + stopifnot(e2 > 0) + + genetic_qt <- standardise(scores[["BETA_QT_SUM"]]) + genetic_bt <- standardise(scores[["BETA_BT_SUM"]]) + + sex_code <- as.integer(sexes[["SEX"]]) + age <- pmin(pmax(round(rnorm(n, mean = 55, sd = 8)), 18), 90) + covariate_effect <- standardise(0.6 * (sex_code == 2) + 0.03 * (age - 55)) + + quantitative <- sqrt(h2) * genetic_qt + + sqrt(c2) * covariate_effect + + sqrt(e2) * rnorm(n) + + liability <- sqrt(h2) * genetic_bt + + sqrt(c2) * covariate_effect + + sqrt(e2) * rnorm(n) + + n_cases <- round(${params.fixture_prevalence} * n) + threshold <- sort(liability, decreasing = TRUE)[n_cases] + binary <- ifelse(liability >= threshold, 2L, 1L) + + pc_names <- paste0("PC", seq_len(${params.fixture_n_pcs})) + pc_values <- lapply(pc_names, function(name) round(pcs[[name]], 6)) + names(pc_values) <- pc_names + + pheno <- data.frame(FID = ids, IID = ids, + QT = round(quantitative, 6), BT = binary, + stringsAsFactors = FALSE) + covar <- data.frame(c(list(FID = ids, IID = ids, + SEX = sex_code, AGE = age), pc_values), + stringsAsFactors = FALSE) + qcovar <- data.frame(c(list(FID = ids, IID = ids, AGE = age), pc_values), + stringsAsFactors = FALSE) + catcovar <- data.frame(FID = ids, IID = ids, SEX = sex_code, + stringsAsFactors = FALSE) + + write_tsv <- function(frame, path) { + write.table(frame, file = path, sep = "\\t", quote = FALSE, + row.names = FALSE, col.names = TRUE) + } + write_tsv(pheno, "${params.fixture_prefix}.pheno") + write_tsv(covar, "${params.fixture_prefix}.covar") + write_tsv(qcovar, "${params.fixture_prefix}.qcovar") + write_tsv(catcovar, "${params.fixture_prefix}.catcovar") + + report <- c( + sprintf("samples\\t%d", n), + sprintf("target_h2\\t%.3f", h2), + sprintf("target_covariate_variance\\t%.3f", c2), + sprintf("target_prevalence\\t%.3f", ${params.fixture_prevalence}), + sprintf("cases\\t%d", sum(binary == 2L)), + sprintf("controls\\t%d", sum(binary == 1L)), + sprintf("cor_QT_genetic_score\\t%.4f", cor(quantitative, genetic_qt)), + sprintf("cor_QT_covariate_effect\\t%.4f", cor(quantitative, covariate_effect)), + sprintf("cor_liability_genetic_score\\t%.4f", cor(liability, genetic_bt)), + sprintf("cor_BT_genetic_score\\t%.4f", cor(binary, genetic_bt)), + sprintf("var_QT_explained_by_genetic_score\\t%.4f", cor(quantitative, genetic_qt)^2), + sprintf("mean_age\\t%.2f", mean(age)), + sprintf("males\\t%d", sum(sex_code == 1L)), + sprintf("females\\t%d", sum(sex_code == 2L)) + ) + writeLines(report, "fixture_summary.txt") + """ + + stub: + """ + printf 'FID\\tIID\\tQT\\tBT\\n' > ${params.fixture_prefix}.pheno + printf 'FID\\tIID\\tSEX\\tAGE\\tPC1\\n' > ${params.fixture_prefix}.covar + printf 'FID\\tIID\\tAGE\\tPC1\\n' > ${params.fixture_prefix}.qcovar + printf 'FID\\tIID\\tSEX\\n' > ${params.fixture_prefix}.catcovar + printf 'samples\\t0\\n' > fixture_summary.txt + """ +} diff --git a/modules/fixture_score_liability.nf b/modules/fixture_score_liability.nf new file mode 100644 index 000000000..2f922b291 --- /dev/null +++ b/modules/fixture_score_liability.nf @@ -0,0 +1,29 @@ +// Compute each sample's genetic value for both simulated traits directly from the +// fixture genotypes, so the simulated signal is carried by the real genotype matrix +// rather than added as noise. +process FIXTURE_SCORE_LIABILITY { + container "community.wave.seqera.io/library/plink2:2.0.0a.6.9--e6710830a4b7f0c6" + + input: + tuple val(prefix), path(pgen), path(pvar), path(psam) + path weights + + output: + path "${prefix}.sscore", emit: sscore + + script: + """ + plink2 \\ + --pfile ${prefix} \\ + --score ${weights} 1 2 header-read cols=+scoresums \\ + --score-col-nums 3-4 \\ + --threads 1 \\ + --seed 1 \\ + --out ${prefix} + """ + + stub: + """ + printf '#FID\\tIID\\tALLELE_CT\\tNAMED_ALLELE_DOSAGE_SUM\\tBETA_QT_AVG\\tBETA_BT_AVG\\tBETA_QT_SUM\\tBETA_BT_SUM\\n' > ${prefix}.sscore + """ +} diff --git a/modules/fixture_select_samples.nf b/modules/fixture_select_samples.nf new file mode 100644 index 000000000..00b7f4034 --- /dev/null +++ b/modules/fixture_select_samples.nf @@ -0,0 +1,48 @@ +// Deterministically select the sample subset used by every GWAS fixture file. +// +// Selection is a fixed stride over the lexicographically sorted sample IDs of the +// source VCF, so the same subset is produced on every run without any RNG. +// The source VCFs carry no sex information (the committed chrX chunk lies entirely +// within PAR1, where both sexes are diploid), so sex is assigned deterministically +// by alternating over the sorted selection. +process FIXTURE_SELECT_SAMPLES { + container "community.wave.seqera.io/library/bcftools_tabix_pip_tools:48085064a9189d8c" + publishDir params.outdir_fixture_pheno_cov, mode: 'copy' + + input: + path vcf_file + + output: + path "fixture_samples.tsv", emit: samples + path "fixture_sex.tsv", emit: sex + + script: + """ + bcftools query -l ${vcf_file} \\ + | LC_ALL=C sort \\ + | awk 'NR % ${params.fixture_sample_stride} == 1' \\ + | head -n ${params.fixture_n_samples} > selected_ids.txt + + selected=\$(wc -l < selected_ids.txt) + if [ "\${selected}" -ne "${params.fixture_n_samples}" ]; then + echo "ERROR: selected \${selected} samples, expected ${params.fixture_n_samples}" >&2 + exit 1 + fi + + printf '#FID\\tIID\\n' > fixture_samples.tsv + awk 'BEGIN { OFS = "\\t" } { print \$1, \$1 }' selected_ids.txt >> fixture_samples.tsv + + printf '#FID\\tIID\\tSEX\\n' > fixture_sex.tsv + awk 'BEGIN { OFS = "\\t" } { print \$1, \$1, (NR % 2 == 1 ? 1 : 2) }' selected_ids.txt >> fixture_sex.tsv + """ + + stub: + """ + printf '#FID\\tIID\\n' > fixture_samples.tsv + printf '#FID\\tIID\\tSEX\\n' > fixture_sex.tsv + for i in 1 2 3; do + printf 'SAMPLE%s\\tSAMPLE%s\\n' "\${i}" "\${i}" >> fixture_samples.tsv + printf 'SAMPLE%s\\tSAMPLE%s\\t1\\n' "\${i}" "\${i}" >> fixture_sex.tsv + done + """ +} diff --git a/modules/fixture_thin_chromosome.nf b/modules/fixture_thin_chromosome.nf new file mode 100644 index 000000000..5b21f5977 --- /dev/null +++ b/modules/fixture_thin_chromosome.nf @@ -0,0 +1,62 @@ +// Build the per-chromosome PLINK 2 fixture from an already-committed chunked VCF. +// +// The sample subset is fixed by FIXTURE_SELECT_SAMPLES, variants are restricted to +// biallelic ACGT SNPs above the fixture MAF floor, and the survivors are LD-thinned +// with plink2 --indep-pairwise. No step here reads the network. +process FIXTURE_THIN_CHROMOSOME { + container "community.wave.seqera.io/library/plink2:2.0.0a.6.9--e6710830a4b7f0c6" + publishDir params.outdir_fixture_genotypes, mode: 'copy', pattern: "*.{pgen,pvar,psam}" + + input: + tuple val(chr), path(vcf_file) + path samples + path sex + + output: + tuple val("${params.fixture_prefix}_${chr}"), path("${params.fixture_prefix}_${chr}.pgen"), path("${params.fixture_prefix}_${chr}.pvar"), path("${params.fixture_prefix}_${chr}.psam"), emit: pgen + + script: + def prefix = "${params.fixture_prefix}_${chr}" + """ + # Sample subset plus basic variant QC. INFO/QUAL/FILTER are dropped from the + # .pvar (pvar-cols=xheader): the source INFO fields describe all 2504 samples + # and would be stale for the 500-sample fixture. + plink2 \\ + --vcf ${vcf_file} \\ + --double-id \\ + --keep ${samples} \\ + --update-sex ${sex} \\ + --snps-only just-acgt \\ + --max-alleles 2 \\ + --set-missing-var-ids '@:#:\$r:\$a' \\ + --rm-dup exclude-all \\ + --maf ${params.fixture_maf} \\ + --threads 1 \\ + --seed 1 \\ + --make-pgen pvar-cols=xheader \\ + --out filtered + + plink2 \\ + --pfile filtered \\ + --indep-pairwise ${params.fixture_ld_window} ${params.fixture_ld_step} ${params.fixture_ld_r2} \\ + --threads 1 \\ + --seed 1 \\ + --out pruned + + plink2 \\ + --pfile filtered \\ + --extract pruned.prune.in \\ + --threads 1 \\ + --seed 1 \\ + --make-pgen pvar-cols=xheader \\ + --out ${prefix} + """ + + stub: + def prefix = "${params.fixture_prefix}_${chr}" + """ + touch ${prefix}.pgen + printf '#CHROM\\tPOS\\tID\\tREF\\tALT\\n' > ${prefix}.pvar + printf '#FID\\tIID\\tSEX\\n' > ${prefix}.psam + """ +} diff --git a/nextflow.config b/nextflow.config index 20308bbec..14faf02f3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -3,6 +3,32 @@ params { outdir_vcfs = "${params.outdir_base}/vcfs" outdir_chunked_vcfs = "${params.outdir_base}/chunked_vcfs" outdir_pheno_cov = "${params.outdir_base}/pheno_cov" + outdir_fixtures = "${params.outdir_base}/fixtures" + outdir_fixture_genotypes = "${params.outdir_fixtures}/genotypes" + outdir_fixture_pheno_cov = "${params.outdir_fixtures}/pheno_cov" + + // Source-data stage. Set to true to regenerate the GWAS fixtures without + // re-downloading the 1000 Genomes release, which is the normal case: the + // chromosome-chunked VCFs the fixtures derive from are already committed. + skip_source_generation = false + + // GWAS fixture generation. Derives from the committed chunked VCFs only. + chunked_vcfs_dir = "${projectDir}/${params.outdir_base}/chunked_vcfs" + fixture_prefix = "example" + fixture_chromosomes = "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22" + fixture_n_samples = 500 + fixture_sample_stride = 5 + fixture_maf = 0.005 + fixture_ld_window = 100 + fixture_ld_step = 10 + fixture_ld_r2 = 0.2 + fixture_n_pcs_computed = 10 + fixture_n_pcs = 5 + fixture_n_causal = 150 + fixture_h2 = 0.5 + fixture_covariate_variance = 0.1 + fixture_prevalence = 0.3 + fixture_seed = 20260101 } // Profile-specific configurations diff --git a/results/fixtures/README.md b/results/fixtures/README.md new file mode 100644 index 000000000..22e764078 --- /dev/null +++ b/results/fixtures/README.md @@ -0,0 +1,212 @@ +# GWAS pipeline fixtures + +Pipeline-level test fixtures for `nf-core/gwas`: one cohort, all 22 autosomes, three +genotype encodings, one signal-bearing quantitative trait, one signal-bearing binary +trait, and a covariate set with sex, age and principal components. + +They exist because the older `results/pheno_cov/` files cannot exercise the current +routes: they are VCF-only, single-chromosome, headerless, have no binary trait, no +sex/age/PC covariates, and a phenotype that is uncorrelated noise, which leaves +variance-component estimators on the boundary of the parameter space. + +## Provenance + +Everything here is derived from `results/chunked_vcfs/chr{1..22}_chunked.vcf.gz`, +which are already committed on this branch (1000 Genomes phase 3, GRCh37/b37, 2504 +samples, the first 4500 variant records of each chromosome). **No step downloads +anything.** + +## Contents + +### `genotypes/` + +Twenty-three bundles — one per autosome plus the merge — each present in all three +encodings, describing exactly the same samples and the same variants: + +| bundle | chromosome | samples | variants | +| --------------- | ---------- | ------- | -------- | +| `example_chr1` | 1 | 500 | 319 | +| `example_chr2` | 2 | 500 | 172 | +| `example_chr3` | 3 | 500 | 181 | +| `example_chr4` | 4 | 500 | 181 | +| `example_chr5` | 5 | 500 | 190 | +| `example_chr6` | 6 | 500 | 269 | +| `example_chr7` | 7 | 500 | 261 | +| `example_chr8` | 8 | 500 | 259 | +| `example_chr9` | 9 | 500 | 203 | +| `example_chr10` | 10 | 500 | 167 | +| `example_chr11` | 11 | 500 | 273 | +| `example_chr12` | 12 | 500 | 274 | +| `example_chr13` | 13 | 500 | 175 | +| `example_chr14` | 14 | 500 | 82 | +| `example_chr15` | 15 | 500 | 178 | +| `example_chr16` | 16 | 500 | 209 | +| `example_chr17` | 17 | 500 | 263 | +| `example_chr18` | 18 | 500 | 223 | +| `example_chr19` | 19 | 500 | 231 | +| `example_chr20` | 20 | 500 | 185 | +| `example_chr21` | 21 | 500 | 362 | +| `example_chr22` | 22 | 500 | 285 | +| `example_all` | 1–22 | 500 | **4942** | + +Encodings per bundle: + +- PLINK 2: `.pgen` + `.pvar` + `.psam` +- PLINK 1: `.bed` + `.bim` + `.fam` +- VCF: `.vcf.gz` + `.vcf.gz.tbi` (bgzip-compressed, tabix-indexed, phased `GT`) + +Both the per-chromosome split and the merged bundle are published: REGENIE and +LDAK-KVIK need more than one chromosome for leave-one-chromosome-out to be +non-degenerate, and the single-cohort routes want one merged bundle. + +Sample identifiers are the bare 1000 Genomes IDs (`HG00096`, …) in every encoding: +`.psam` `IID`, `.fam` column 2, and the VCF `#CHROM` sample columns all carry the same +string, and it matches the `IID` column of everything under `pheno_cov/`. The PLINK +filesets also carry an `FID`, set equal to the `IID`; the VCFs are exported with +`--export vcf id-paste=iid` so the `FID` is not pasted onto the sample name. That +matters for the VCF association route, where the genotypes are passed as `--vcf` and +joined to a phenotype file by `IID`. + +Sample sex is recorded in `.psam` and `.fam` (1 = male, 2 = female). + +### `pheno_cov/` + +| file | header | description | +| --------------------- | -------------------------- | ------------------------------------------------------- | +| `example.pheno` | `FID IID QT BT` | quantitative trait and binary trait | +| `example.covar` | `FID IID SEX AGE PC1..PC5` | all covariates in one file | +| `example.qcovar` | `FID IID AGE PC1..PC5` | quantitative covariates only | +| `example.catcovar` | `FID IID SEX` | categorical covariates only | +| `fixture_samples.tsv` | `#FID IID` | the selected 500 samples | +| `fixture_sex.tsv` | `#FID IID SEX` | the sex assignment | +| `causal_weights.tsv` | `ID A1 BETA_QT BETA_BT` | the simulated causal effects (ALT is the effect allele) | +| `fixture_summary.txt` | — | realised properties of the simulation | + +All files are tab-delimited. `BT` uses the PLINK convention, `1` = control, +`2` = case. GCTA and LDAK want headerless phenotype files, so the pipeline is +expected to normalise these before use. `gcta --fastGWA-mlm-binary` additionally +wants `0`/`1` rather than `1`/`2` and errors with `XtWX is not invertible` on the +PLINK coding, so that route needs the recode as well as the header strip. + +## How the data were built + +1. **Samples.** The 2504 source sample IDs are sorted with `LC_ALL=C sort` and + every 5th is taken until 500 are selected. There is no RNG in the selection. +2. **Sex.** The source VCFs carry no sex, and the committed chrX chunk lies + entirely in PAR1 where both sexes are diploid, so sex cannot be recovered from + the data; it is assigned by alternating over the sorted selection, giving 250 + males and 250 females. +3. **Variants.** Per chromosome, `plink2` keeps biallelic ACGT SNPs with unique + IDs and MAF ≥ 0.005, then LD-thins with `--indep-pairwise 100 10 0.2`. `INFO`, + `QUAL` and `FILTER` are dropped, because the source `INFO` describes all 2504 + samples and is stale for a 500-sample subset. Variants without an rsID are + named `CHROM:POS:REF:ALT`. +4. **Merge and PCA.** The 22 per-chromosome bundles are merged with + `--pmerge-list`, and ten principal components are computed from the merged + bundle with exact (non-approximate) `plink2 --pca`. +5. **Genetic values.** Two disjoint sets of 150 causal variants are drawn from the + merged bundle with effect sizes drawn from N(0, 1) under a fixed seed, one set + for the quantitative trait and one for the binary trait's liability. Each + sample's genetic value is computed from the actual genotypes with + `plink2 --score`. +6. **Traits.** Both the quantitative trait and the binary liability are built as + + ``` + sqrt(0.5) * standardised genetic score + + sqrt(0.1) * standardised covariate effect (sex and age) + + sqrt(0.4) * N(0, 1) noise + ``` + + so the target heritability is 0.5 on the total-variance scale and the supplied + covariates genuinely matter. The binary trait dichotomises the liability at the + empirical quantile that gives exactly the target prevalence, so the case count + is fixed rather than sampled. + +## Chromosome coverage and the LD threshold + +The fixture covers all 22 autosomes rather than a handful, and that is what makes +the LD thinning real. The source chunks are the _first_ 4500 variant records of each +chromosome, which span 0.773 Mb on chr1 but only 0.128 Mb on chr2 and 0.104 Mb on +chr3 — 100–130 kb windows holding 4500 variants each, i.e. essentially one LD block +per chromosome. Within such a window independence is absent from the data rather +than merely under-filtered, so no r² threshold recovers it: the number of genuinely +independent variants tracks the number of _chromosomes_ used, not the number of +variants kept. Cross-chromosome variants are unlinked by construction, so widening +to 22 autosomes buys independence proportional to chromosome count while +simultaneously lifting the variant count. + +A hard floor applies: `gcta/fastgwa`'s binary-trait path needs at least 2000 +autosomal SNPs for tuning and aborts with `can't read 2000 SNPs from the autosomes +for tuning` below that. + +Generation started at `100 10 0.2`, with relaxation required only if the 2000-variant +floor was missed: + +| `--indep-pairwise` | chromosomes | surviving variants | verdict | +| ------------------ | ----------- | ------------------ | ------------------------------------------- | +| `100 10 0.2` | 1–22 | **4942** | **chosen** — conventional r², clears 2000 | +| `100 10 0.9` | 1–3 | 1706 | previous fixture; below the floor, rejected | + +`100 10 0.2` is the conventional pruning threshold and was the initial +point; because it cleared the floor by a wide margin on that first run, no relaxation +was needed and none was applied. It ships because it is that starting point and it +worked, not because tighter thresholds were run and 0.2 came out best — no threshold +below 0.2 was tested against the 22-autosome input. As a known-headroom note rather +than a systematic sweep, `100 10 0.1` was independently run once against the same +input and also clears the floor, at 3801 variants; nothing tighter than 0.1 has been +tried. The 0.9/three-chromosome row is the fixture this one replaces, kept as the +measurement that motivated the change. + +Verified against `gcta64` directly: `--fastGWA-mlm-binary` on the previous +1706-variant merged bundle fails with `can't read 2000 SNPs from the autosomes for +tuning`, while on this 4942-variant bundle it completes and writes results for all +4942 SNPs. + +## Realised properties + +From `pheno_cov/fixture_summary.txt`: + +``` +samples 500 +cases / controls 150 / 350 (prevalence 0.30) +males / females 250 / 250 +cor(QT, genetic score) 0.6983 -> r2 = 0.4876 +cor(liability, genetic score) 0.7106 +cor(BT, genetic score) 0.5231 +mean age 54.84 +``` + +A `plink2 --glm` run of `QT` on `example_all` with `SEX`, `AGE` and `PC1..PC5` as +covariates gives a minimum p-value of 7.5e-6 over the 4942 tests, one variant below +the Bonferroni threshold (0.05/4942 = 1.0e-5) and ten below 1e-3. Per-variant +p-values are weaker than the previous three-chromosome fixture's 1.0e-12 precisely +because the thinning is now genuine: at r² = 0.2 the 150 causal variants are no +longer shadowed by near-duplicate tags, and the same simulated heritability is +spread over 4942 independent tests instead of 1706 correlated ones. The trait-level +signal is unchanged (the genetic score still explains 49% of `QT`'s variance), so +heritability and mixed-model routes see the same effect; only single-variant +significance is diluted. + +## Regenerating + +From the root of this branch: + +```bash +nextflow run main.nf -profile test --skip_source_generation +``` + +`--skip_source_generation` skips the 1000 Genomes download and chunking stage, +whose output is already committed under `results/chunked_vcfs/`. Everything under +`results/fixtures/` is rewritten in place, as real copies rather than symlinks. + +The output is byte-for-byte reproducible: every RNG draw goes through a fixed seed +with R's RNG kind pinned explicitly, `plink2` is run single-threaded with a fixed +seed, sample selection and merge order are deterministic, and the run-date header +`plink2` writes into exported VCFs is stripped before compression. Two independent +runs of the command above, into separate output and work directories, produce +byte-identical copies of all 192 generated files. + +The simulation is controlled by the `fixture_*` parameters in `nextflow.config` +(chromosomes, sample count, MAF floor, LD thinning, causal-variant count, +heritability, covariate variance, prevalence, seed). Changing any of them changes +the fixtures, and any pipeline snapshot taken against them has to be regenerated. diff --git a/results/fixtures/genotypes/example_all.bed b/results/fixtures/genotypes/example_all.bed new file mode 100644 index 000000000..33e2068a8 Binary files /dev/null and b/results/fixtures/genotypes/example_all.bed differ diff --git a/results/fixtures/genotypes/example_all.bim b/results/fixtures/genotypes/example_all.bim new file mode 100644 index 000000000..0e24a8228 --- /dev/null +++ b/results/fixtures/genotypes/example_all.bim @@ -0,0 +1,4942 @@ +1 1:11008:C:G 0 11008 G C +1 1:13110:G:A 0 13110 A G +1 1:13116:T:G 0 13116 G T +1 1:13273:G:C 0 13273 C G +1 1:13550:G:A 0 13550 A G +1 1:14599:T:A 0 14599 A T +1 1:14930:A:G 0 14930 G A +1 1:14933:G:A 0 14933 A G +1 1:15211:T:G 0 15211 G T +1 1:15245:C:T 0 15245 T C +1 1:15774:G:A 0 15774 A G +1 1:15777:A:G 0 15777 G A +1 1:15820:G:T 0 15820 T G +1 1:16949:A:C 0 16949 C A +1 1:18849:C:G 0 18849 G C +1 1:30923:G:T 0 30923 T 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b/results/fixtures/genotypes/example_chr5.psam new file mode 100644 index 000000000..abb3b27e4 --- /dev/null +++ b/results/fixtures/genotypes/example_chr5.psam @@ -0,0 +1,501 @@ +#FID IID SEX +HG00096 HG00096 1 +HG00102 HG00102 2 +HG00108 HG00108 1 +HG00113 HG00113 2 +HG00118 HG00118 1 +HG00123 HG00123 2 +HG00129 HG00129 1 +HG00136 HG00136 2 +HG00141 HG00141 1 +HG00148 HG00148 2 +HG00155 HG00155 1 +HG00171 HG00171 2 +HG00178 HG00178 1 +HG00183 HG00183 2 +HG00189 HG00189 1 +HG00234 HG00234 2 +HG00239 HG00239 1 +HG00245 HG00245 2 +HG00253 HG00253 1 +HG00258 HG00258 2 +HG00263 HG00263 1 +HG00268 HG00268 2 +HG00274 HG00274 1 +HG00280 HG00280 2 +HG00288 HG00288 1 +HG00309 HG00309 2 +HG00318 HG00318 1 +HG00324 HG00324 2 +HG00329 HG00329 1 +HG00335 HG00335 2 +HG00341 HG00341 1 +HG00346 HG00346 2 +HG00355 HG00355 1 +HG00361 HG00361 2 +HG00367 HG00367 1 +HG00373 HG00373 2 +HG00380 HG00380 1 +HG00403 HG00403 2 +HG00410 HG00410 1 +HG00436 HG00436 2 +HG00446 HG00446 1 +HG00457 HG00457 2 +HG00473 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a/results/fixtures/pheno_cov/example.covar b/results/fixtures/pheno_cov/example.covar new file mode 100644 index 000000000..f12f4805e --- /dev/null +++ b/results/fixtures/pheno_cov/example.covar @@ -0,0 +1,501 @@ +FID IID SEX AGE PC1 PC2 PC3 PC4 PC5 +HG00096 HG00096 1 51 0.028896 0.063982 0.003938 0.035779 -0.000446 +HG00102 HG00102 2 59 0.023761 0.062907 -0.006643 0.074024 0.00961 +HG00108 HG00108 1 43 0.02562 0.06192 -0.001934 0.058495 0.005605 +HG00113 HG00113 2 45 0.022467 0.058848 0.011655 0.084828 -0.011338 +HG00118 HG00118 1 53 0.021782 0.053723 -0.005816 0.035392 0.024289 +HG00123 HG00123 2 47 0.0255 0.065202 0.021024 0.078872 -0.002047 +HG00129 HG00129 1 42 0.024463 0.047822 -0.010547 0.023903 0.015699 +HG00136 HG00136 2 53 0.029197 0.048067 0.02083 0.039614 0.015933 +HG00141 HG00141 1 69 0.026473 0.059388 0.014128 0.057451 0.002639 +HG00148 HG00148 2 56 0.028171 0.050639 0.001999 0.031114 -0.01074 +HG00155 HG00155 1 58 0.025329 0.043667 -0.005343 0.035908 -0.003074 +HG00171 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b/results/fixtures/relational/analysis_manifest_association_only.csv new file mode 100644 index 000000000..b53294ce9 --- /dev/null +++ b/results/fixtures/relational/analysis_manifest_association_only.csv @@ -0,0 +1,2 @@ +analysis_id,cohort_id,trait_id,trait_type,phenotype,phenotype_column,control_value,case_value,quant_covariates,cat_covariates,association_methods,heritability_methods,population_prevalence +example_association,example_cohort,QT,quantitative,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.pheno,QT,,,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.qcovar,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.catcovar,"plink2,regenie,gcta_fastgwa,ldak_kvik",, diff --git a/results/fixtures/relational/analysis_manifest_binary.csv b/results/fixtures/relational/analysis_manifest_binary.csv new file mode 100644 index 000000000..dd2cb0166 --- /dev/null +++ b/results/fixtures/relational/analysis_manifest_binary.csv @@ -0,0 +1,2 @@ +analysis_id,cohort_id,trait_id,trait_type,phenotype,phenotype_column,control_value,case_value,quant_covariates,cat_covariates,association_methods,heritability_methods,population_prevalence +example_binary,example_cohort,BT,binary,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.pheno,BT,1,2,,,plink2,, diff --git a/results/fixtures/relational/analysis_manifest_heritability_only.csv b/results/fixtures/relational/analysis_manifest_heritability_only.csv new file mode 100644 index 000000000..8caace2c8 --- /dev/null +++ b/results/fixtures/relational/analysis_manifest_heritability_only.csv @@ -0,0 +1,2 @@ +analysis_id,cohort_id,trait_id,trait_type,phenotype,phenotype_column,control_value,case_value,quant_covariates,cat_covariates,association_methods,heritability_methods,population_prevalence +example_heritability,example_cohort,BT,binary,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.pheno,BT,1,2,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.qcovar,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.catcovar,,"gcta_greml,gcta_greml_ldms,ldak_reml,ldak_he,ldak_pcgc",0.1 diff --git a/results/fixtures/relational/analysis_manifest_heterogeneous.csv b/results/fixtures/relational/analysis_manifest_heterogeneous.csv new file mode 100644 index 000000000..481c35ef1 --- /dev/null +++ b/results/fixtures/relational/analysis_manifest_heterogeneous.csv @@ -0,0 +1,3 @@ +analysis_id,cohort_id,trait_id,trait_type,phenotype,phenotype_column,control_value,case_value,quant_covariates,cat_covariates,association_methods,heritability_methods,population_prevalence +heterogeneous_qt,example_cohort,QT,quantitative,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.pheno,QT,,,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.qcovar,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.catcovar,"plink2,regenie,gcta_fastgwa,ldak_kvik","gcta_greml,gcta_greml_ldms,ldak_reml,ldak_he", +heterogeneous_bt,example_cohort,BT,binary,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.pheno,BT,1,2,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.qcovar,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.catcovar,"plink2,gcta_fastgwa,ldak_kvik","gcta_greml,gcta_greml_ldms,ldak_reml,ldak_he,ldak_pcgc",0.1 diff --git a/results/fixtures/relational/analysis_manifest_quantitative.csv b/results/fixtures/relational/analysis_manifest_quantitative.csv new file mode 100644 index 000000000..732225cb2 --- /dev/null +++ b/results/fixtures/relational/analysis_manifest_quantitative.csv @@ -0,0 +1,2 @@ +analysis_id,cohort_id,trait_id,trait_type,phenotype,phenotype_column,control_value,case_value,quant_covariates,cat_covariates,association_methods,heritability_methods,population_prevalence +example_quantitative,example_cohort,QT,quantitative,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/pheno_cov/example.pheno,QT,,,,,plink2,, diff --git a/results/fixtures/relational/cohort_manifest.csv b/results/fixtures/relational/cohort_manifest.csv new file mode 100644 index 000000000..0015af03b --- /dev/null +++ b/results/fixtures/relational/cohort_manifest.csv @@ -0,0 +1,2 @@ +cohort_id,genome_build,ancestry,pgen,psam,pvar,bed,bim,fam,vcf +example_cohort,GRCh37,EUR,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/genotypes/example_all.pgen,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/genotypes/example_all.psam,https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/genotypes/example_all.pvar,,,, diff --git a/results/fixtures/relational/method_options_heterogeneous.json b/results/fixtures/relational/method_options_heterogeneous.json new file mode 100644 index 000000000..2a5671184 --- /dev/null +++ b/results/fixtures/relational/method_options_heterogeneous.json @@ -0,0 +1,37 @@ +{ + "heterogeneous_qt": { + "gcta": { + "grm_maf": 0.01, + "grm_extract": "https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/relational/resources/gcta_grm_extract.txt", + "reml_no_constrain": true, + "sparse_cutoff": 0.025, + "ld_score_region_kb": 100, + "ld_bins": 2, + "ldms_maf_edges": [0, 0.01, 0.05, 0.5] + }, + "ldak": { + "model": "custom", + "power": -0.5, + "weights_policy": "provided", + "weights": "https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/relational/resources/ldak_weights.txt", + "relatedness_filter": true, + "kvik_step1_subset": "provided", + "predictor_extract": "https://raw.githubusercontent.com/nf-core/test-datasets/gwas/results/fixtures/relational/resources/ldak_predictor_extract.txt" + } + }, + "heterogeneous_bt": { + "gcta": { + "sparse_cutoff": 0.05, + "ld_score_region_kb": 200, + "ld_bins": 4, + "ldms_maf_edges": [0, 0.01, 0.05, 0.2, 0.5] + }, + "ldak": { + "model": "human_default", + "power": -0.25, + "weights_policy": "equal", + "relatedness_filter": false, + "kvik_step1_subset": "all" + } + } +} diff --git a/results/fixtures/relational/resources/gcta_grm_extract.txt b/results/fixtures/relational/resources/gcta_grm_extract.txt new file mode 100644 index 000000000..bb14eb24e --- /dev/null +++ b/results/fixtures/relational/resources/gcta_grm_extract.txt @@ -0,0 +1,3 @@ +1:11008:C:G +1:13110:G:A +1:13116:T:G diff --git a/results/fixtures/relational/resources/ldak_predictor_extract.txt b/results/fixtures/relational/resources/ldak_predictor_extract.txt new file mode 100644 index 000000000..bb14eb24e --- /dev/null +++ b/results/fixtures/relational/resources/ldak_predictor_extract.txt @@ -0,0 +1,3 @@ +1:11008:C:G +1:13110:G:A +1:13116:T:G diff --git a/results/fixtures/relational/resources/ldak_weights.txt b/results/fixtures/relational/resources/ldak_weights.txt new file mode 100644 index 000000000..5eb1a14f5 --- /dev/null +++ b/results/fixtures/relational/resources/ldak_weights.txt @@ -0,0 +1,3 @@ +1:11008:C:G 1 +1:13110:G:A 1 +1:13116:T:G 1 diff --git a/tests/main.nf.test b/tests/main.nf.test index 2ca7f2355..befad35e8 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -18,8 +18,12 @@ nextflow_pipeline { // Assert that the workflow exited with status 0 (no error) assert workflow.exitStatus == 0 - // Assert that exactly 8 processes were run in the workflow - assert workflow.trace.tasks().size() == 8, "Expected 8 processes, got ${workflow.trace.tasks().size()}" + // Assert that exactly 82 processes were run in the workflow: + // 8 for the source-data stage (download, chunk, index, concat, sample IDs, + // legacy pheno/cov) and 74 for the GWAS fixture stage (sample selection, + // 22 x per-chromosome thinning, merge, PCA, causal weights, scoring, + // pheno/covar, 23 x format export, 23 x VCF compression) + assert workflow.trace.tasks().size() == 82, "Expected 82 processes, got ${workflow.trace.tasks().size()}" // Snapshot test: capture the relative paths of all files produced in the workDir // - path("${workDir}").list() lists all files/directories in the work directory diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 39775f3be..eab5cceda 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -10,6 +10,91 @@ ".command.begin", ".command.begin", ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.begin", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", ".command.err", ".command.err", ".command.err", @@ -18,6 +103,91 @@ ".command.err", ".command.err", ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + ".command.err", + 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".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", ".command.log", ".command.log", ".command.log", @@ -26,6 +196,91 @@ ".command.log", ".command.log", ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.log", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", ".command.out", ".command.out", ".command.out", @@ -34,6 +289,91 @@ ".command.out", ".command.out", ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.out", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", ".command.run", ".command.run", ".command.run", @@ -42,6 +382,70 @@ ".command.run", ".command.run", ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.run", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", ".command.sh", ".command.sh", ".command.sh", @@ -50,6 +454,70 @@ ".command.sh", ".command.sh", ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.sh", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", ".command.trace", ".command.trace", ".command.trace", @@ -58,6 +526,130 @@ ".command.trace", ".command.trace", ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".command.trace", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", + ".exitcode", ".exitcode", ".exitcode", ".exitcode", @@ -70,19 +662,473 @@ "ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz", "ALL.chrX.phase3_shapeit2_mvncall_integrated_v1c.20130502.genotypes.vcf.gz", "ALL.chrX.phase3_shapeit2_mvncall_integrated_v1c.20130502.genotypes.vcf.gz", + "causal_weights.tsv", + "causal_weights.tsv", + "chr10_chunked.vcf.gz", + "chr11_chunked.vcf.gz", + "chr12_chunked.vcf.gz", + "chr13_chunked.vcf.gz", + "chr14_chunked.vcf.gz", + "chr15_chunked.vcf.gz", + "chr16_chunked.vcf.gz", + "chr17_chunked.vcf.gz", + "chr18_chunked.vcf.gz", + "chr19_chunked.vcf.gz", + "chr1_chunked.vcf.gz", + "chr1_chunked.vcf.gz", "chr1_chunked.vcf.gz", "chr1_chunked.vcf.gz", "chr1_chunked.vcf.gz", "chr1_chunked.vcf.gz", "chr1_chunked.vcf.gz.tbi", + "chr20_chunked.vcf.gz", + "chr21_chunked.vcf.gz", + "chr22_chunked.vcf.gz", + "chr2_chunked.vcf.gz", + "chr3_chunked.vcf.gz", + "chr4_chunked.vcf.gz", + "chr5_chunked.vcf.gz", + "chr6_chunked.vcf.gz", + "chr7_chunked.vcf.gz", + "chr8_chunked.vcf.gz", + "chr9_chunked.vcf.gz", "chrX_chunked.vcf.gz", "chrX_chunked.vcf.gz", "chrX_chunked.vcf.gz", "chrX_chunked.vcf.gz.tbi", "combined_chunked.vcf.gz", "combined_chunked.vcf.gz.tbi", + "example.catcovar", "example.covar", + "example.covar", + "example.pheno", "example.pheno", + "example.qcovar", + "example_all.bed", + "example_all.bim", + "example_all.eigenval", + "example_all.eigenvec", + "example_all.eigenvec", + "example_all.fam", + "example_all.pgen", + "example_all.pgen", + "example_all.pgen", + "example_all.pgen", + "example_all.psam", + "example_all.psam", + "example_all.psam", + "example_all.psam", + "example_all.pvar", + "example_all.pvar", + "example_all.pvar", + "example_all.pvar", + "example_all.pvar", + "example_all.sscore", + "example_all.sscore", + "example_all.vcf", + "example_all.vcf", + "example_all.vcf.gz", + "example_all.vcf.gz.tbi", + "example_chr1.bed", + "example_chr1.bim", + "example_chr1.fam", + "example_chr1.pgen", + "example_chr1.pgen", + "example_chr1.pgen", + "example_chr1.psam", + "example_chr1.psam", + "example_chr1.psam", + "example_chr1.pvar", + "example_chr1.pvar", + "example_chr1.pvar", + "example_chr1.vcf", + "example_chr1.vcf", + "example_chr1.vcf.gz", + "example_chr1.vcf.gz.tbi", + "example_chr10.bed", + "example_chr10.bim", + "example_chr10.fam", + "example_chr10.pgen", + "example_chr10.pgen", + "example_chr10.pgen", + "example_chr10.psam", + "example_chr10.psam", + "example_chr10.psam", + "example_chr10.pvar", + "example_chr10.pvar", + "example_chr10.pvar", + "example_chr10.vcf", + "example_chr10.vcf", + "example_chr10.vcf.gz", + "example_chr10.vcf.gz.tbi", + "example_chr11.bed", + "example_chr11.bim", + "example_chr11.fam", + "example_chr11.pgen", + "example_chr11.pgen", + "example_chr11.pgen", + "example_chr11.psam", + "example_chr11.psam", + "example_chr11.psam", + "example_chr11.pvar", + "example_chr11.pvar", + "example_chr11.pvar", + "example_chr11.vcf", + "example_chr11.vcf", + "example_chr11.vcf.gz", + "example_chr11.vcf.gz.tbi", + "example_chr12.bed", + "example_chr12.bim", + "example_chr12.fam", + "example_chr12.pgen", + "example_chr12.pgen", + "example_chr12.pgen", + "example_chr12.psam", + "example_chr12.psam", + "example_chr12.psam", + "example_chr12.pvar", + "example_chr12.pvar", + "example_chr12.pvar", + "example_chr12.vcf", + "example_chr12.vcf", + "example_chr12.vcf.gz", + "example_chr12.vcf.gz.tbi", + "example_chr13.bed", + "example_chr13.bim", + "example_chr13.fam", + "example_chr13.pgen", + "example_chr13.pgen", + "example_chr13.pgen", + "example_chr13.psam", + "example_chr13.psam", + "example_chr13.psam", + "example_chr13.pvar", + "example_chr13.pvar", + "example_chr13.pvar", + "example_chr13.vcf", + "example_chr13.vcf", + "example_chr13.vcf.gz", + "example_chr13.vcf.gz.tbi", + "example_chr14.bed", + "example_chr14.bim", + "example_chr14.fam", + "example_chr14.pgen", + "example_chr14.pgen", + "example_chr14.pgen", + "example_chr14.psam", + "example_chr14.psam", + "example_chr14.psam", + "example_chr14.pvar", + "example_chr14.pvar", + "example_chr14.pvar", + "example_chr14.vcf", + "example_chr14.vcf", + "example_chr14.vcf.gz", + "example_chr14.vcf.gz.tbi", + "example_chr15.bed", + "example_chr15.bim", + "example_chr15.fam", + "example_chr15.pgen", + "example_chr15.pgen", + "example_chr15.pgen", + "example_chr15.psam", + "example_chr15.psam", + "example_chr15.psam", + "example_chr15.pvar", + "example_chr15.pvar", + "example_chr15.pvar", + "example_chr15.vcf", + "example_chr15.vcf", + "example_chr15.vcf.gz", + "example_chr15.vcf.gz.tbi", + "example_chr16.bed", + "example_chr16.bim", + "example_chr16.fam", + "example_chr16.pgen", + "example_chr16.pgen", + "example_chr16.pgen", + "example_chr16.psam", + "example_chr16.psam", + "example_chr16.psam", + "example_chr16.pvar", + "example_chr16.pvar", + "example_chr16.pvar", + "example_chr16.vcf", + "example_chr16.vcf", + "example_chr16.vcf.gz", + "example_chr16.vcf.gz.tbi", + "example_chr17.bed", + "example_chr17.bim", + "example_chr17.fam", + "example_chr17.pgen", + "example_chr17.pgen", + "example_chr17.pgen", + "example_chr17.psam", + "example_chr17.psam", + "example_chr17.psam", + "example_chr17.pvar", + "example_chr17.pvar", + "example_chr17.pvar", + "example_chr17.vcf", + "example_chr17.vcf", + "example_chr17.vcf.gz", + "example_chr17.vcf.gz.tbi", + "example_chr18.bed", + "example_chr18.bim", + "example_chr18.fam", + "example_chr18.pgen", + "example_chr18.pgen", + "example_chr18.pgen", + "example_chr18.psam", + "example_chr18.psam", + "example_chr18.psam", + "example_chr18.pvar", + "example_chr18.pvar", + "example_chr18.pvar", + "example_chr18.vcf", + "example_chr18.vcf", + "example_chr18.vcf.gz", + "example_chr18.vcf.gz.tbi", + "example_chr19.bed", + "example_chr19.bim", + "example_chr19.fam", + "example_chr19.pgen", + "example_chr19.pgen", + "example_chr19.pgen", + "example_chr19.psam", + "example_chr19.psam", + "example_chr19.psam", + "example_chr19.pvar", + "example_chr19.pvar", + "example_chr19.pvar", + "example_chr19.vcf", + "example_chr19.vcf", + "example_chr19.vcf.gz", + "example_chr19.vcf.gz.tbi", + "example_chr2.bed", + "example_chr2.bim", + "example_chr2.fam", + "example_chr2.pgen", + "example_chr2.pgen", + "example_chr2.pgen", + "example_chr2.psam", + "example_chr2.psam", + "example_chr2.psam", + "example_chr2.pvar", + "example_chr2.pvar", + "example_chr2.pvar", + "example_chr2.vcf", + "example_chr2.vcf", + "example_chr2.vcf.gz", + "example_chr2.vcf.gz.tbi", + "example_chr20.bed", + "example_chr20.bim", + "example_chr20.fam", + "example_chr20.pgen", + "example_chr20.pgen", + "example_chr20.pgen", + "example_chr20.psam", + "example_chr20.psam", + "example_chr20.psam", + "example_chr20.pvar", + "example_chr20.pvar", + "example_chr20.pvar", + "example_chr20.vcf", + "example_chr20.vcf", + "example_chr20.vcf.gz", + "example_chr20.vcf.gz.tbi", + "example_chr21.bed", + "example_chr21.bim", + "example_chr21.fam", + "example_chr21.pgen", + "example_chr21.pgen", + "example_chr21.pgen", + "example_chr21.psam", + "example_chr21.psam", + "example_chr21.psam", + "example_chr21.pvar", + "example_chr21.pvar", + "example_chr21.pvar", + "example_chr21.vcf", + "example_chr21.vcf", + "example_chr21.vcf.gz", + "example_chr21.vcf.gz.tbi", + "example_chr22.bed", + "example_chr22.bim", + "example_chr22.fam", + "example_chr22.pgen", + "example_chr22.pgen", + "example_chr22.pgen", + "example_chr22.psam", + "example_chr22.psam", + "example_chr22.psam", + "example_chr22.pvar", + "example_chr22.pvar", + "example_chr22.pvar", + "example_chr22.vcf", + "example_chr22.vcf", + "example_chr22.vcf.gz", + "example_chr22.vcf.gz.tbi", + "example_chr3.bed", + "example_chr3.bim", + "example_chr3.fam", + "example_chr3.pgen", + "example_chr3.pgen", + "example_chr3.pgen", + "example_chr3.psam", + "example_chr3.psam", + "example_chr3.psam", + "example_chr3.pvar", + "example_chr3.pvar", + "example_chr3.pvar", + "example_chr3.vcf", + "example_chr3.vcf", + "example_chr3.vcf.gz", + "example_chr3.vcf.gz.tbi", + "example_chr4.bed", + "example_chr4.bim", + "example_chr4.fam", + "example_chr4.pgen", + "example_chr4.pgen", + "example_chr4.pgen", + "example_chr4.psam", + "example_chr4.psam", + "example_chr4.psam", + "example_chr4.pvar", + "example_chr4.pvar", + "example_chr4.pvar", + "example_chr4.vcf", + "example_chr4.vcf", + "example_chr4.vcf.gz", + "example_chr4.vcf.gz.tbi", + "example_chr5.bed", + "example_chr5.bim", + "example_chr5.fam", + "example_chr5.pgen", + "example_chr5.pgen", + "example_chr5.pgen", + "example_chr5.psam", + "example_chr5.psam", + "example_chr5.psam", + "example_chr5.pvar", + "example_chr5.pvar", + "example_chr5.pvar", + "example_chr5.vcf", + "example_chr5.vcf", + "example_chr5.vcf.gz", + "example_chr5.vcf.gz.tbi", + "example_chr6.bed", + "example_chr6.bim", + "example_chr6.fam", + "example_chr6.pgen", + "example_chr6.pgen", + "example_chr6.pgen", + "example_chr6.psam", + "example_chr6.psam", + "example_chr6.psam", + "example_chr6.pvar", + "example_chr6.pvar", + "example_chr6.pvar", + "example_chr6.vcf", + "example_chr6.vcf", + "example_chr6.vcf.gz", + "example_chr6.vcf.gz.tbi", + "example_chr7.bed", + "example_chr7.bim", + "example_chr7.fam", + "example_chr7.pgen", + "example_chr7.pgen", + "example_chr7.pgen", + "example_chr7.psam", + "example_chr7.psam", + "example_chr7.psam", + "example_chr7.pvar", + "example_chr7.pvar", + "example_chr7.pvar", + "example_chr7.vcf", + "example_chr7.vcf", + "example_chr7.vcf.gz", + "example_chr7.vcf.gz.tbi", + "example_chr8.bed", + "example_chr8.bim", + "example_chr8.fam", + "example_chr8.pgen", + "example_chr8.pgen", + "example_chr8.pgen", + "example_chr8.psam", + "example_chr8.psam", + "example_chr8.psam", + "example_chr8.pvar", + "example_chr8.pvar", + "example_chr8.pvar", + "example_chr8.vcf", + "example_chr8.vcf", + "example_chr8.vcf.gz", + "example_chr8.vcf.gz.tbi", + "example_chr9.bed", + "example_chr9.bim", + "example_chr9.fam", + "example_chr9.pgen", + "example_chr9.pgen", + "example_chr9.pgen", + "example_chr9.psam", + "example_chr9.psam", + "example_chr9.psam", + "example_chr9.pvar", + "example_chr9.pvar", + "example_chr9.pvar", + "example_chr9.vcf", + "example_chr9.vcf", + "example_chr9.vcf.gz", + "example_chr9.vcf.gz.tbi", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_samples.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_sex.tsv", + "fixture_summary.txt", "header.txt", "header.txt", "results/vcfs/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz", @@ -94,9 +1140,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.4" }, - "timestamp": "2025-07-02T15:50:26.8231" + "timestamp": "2026-07-28T05:26:30.544911721" } } \ No newline at end of file