diff --git a/CHANGELOG.md b/CHANGELOG.md index 3a1b8d40..c5d51369 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,6 +64,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Update and simplify subworkflows snapshot and check only for files names (no md5sum for bam and vcf files due to timestamp). - [#157](https://github.com/nf-core/phaseimpute/pull/157) - Add `chunk_model` as parameter for better control over `GLIMPSE2_CHUNK` and set window size in `GLIMPSE1_CHUNK` and `GLIMPSE2_chunk` to 4mb to reduce number of chunks (empirical). - [#160](https://github.com/nf-core/phaseimpute/pull/160) - Improve `CHANGELOG.md` and add details to `usage.md` +- [#158](https://github.com/nf-core/phaseimpute/pull/158) - Remove frequency computation and phasing from full test to reduce cost and computational time. ### `Fixed` @@ -73,6 +74,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza - [#75](https://github.com/nf-core/phaseimpute/pull/75) - Set frequency computation with `VCFFIXUP` process as optional with `--compute_freq`. Use `GLIMPSE_CHUNK` on panel vcf to compute the chunk and not makewindows on fasta. - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV. - [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`. +- [#158](https://github.com/nf-core/phaseimpute/pull/158) - Fix contigs usage when regions is only a subset of the given contigs (e.g. if panel file has the 22 chr and the region file only 2 then only the 2 common will be processed). Fix `multiQC` samples names for better comprehension. Fix `-resume` errors when `ch_fasta` is use by adding `cache = 'lenient'` in necessary processes. Fix `--window-size` of `GLIMPSE_CHUNK` from `4` to `4000000`. - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input. - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 033877b8..75c911d4 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -17,3 +17,10 @@ top_modules: export_plots: true disable_version_detection: true + +fn_clean_trim: + - ".panel" + +extra_fn_clean_exts: + - type: regex + pattern: "\\.batch[0-9]+" diff --git a/conf/modules.config b/conf/modules.config index 65d412dd..74062fa8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -31,11 +31,13 @@ process { // Simulation // Coverage process withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_INP' { - ext.prefix = { "${meta.id}.A-truth" } + cache = "lenient" + ext.prefix = { "${meta.id}.truth" } publishDir = [ enabled: false ] } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_DWN' { - ext.prefix = { "${meta.id}.B-sim" } + cache = "lenient" + ext.prefix = { "${meta.id}" } publishDir = [ enabled: false ] } @@ -75,7 +77,7 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:LIST_TO_FILE' { tag = { "${meta.id}" } - ext.prefix = { "${meta.id}.${meta.batch}" } + ext.prefix = { "${meta.id}.batch${meta.batch}" } publishDir = [ path: { "${params.outdir}/imputation/batch" }, mode: params.publish_dir_mode, diff --git a/conf/steps/imputation_glimpse1.config b/conf/steps/imputation_glimpse1.config index 29e8f6b2..d28ad992 100644 --- a/conf/steps/imputation_glimpse1.config +++ b/conf/steps/imputation_glimpse1.config @@ -26,6 +26,7 @@ process { } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_GLIMPSE1:BCFTOOLS_MPILEUP' { + cache = "lenient" ext.args = [ "-I", "-E", @@ -39,6 +40,7 @@ process { } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_GLIMPSE1:BCFTOOLS_MERGE' { + cache = "lenient" ext.args = [ "--write-index=tbi", ].join(' ') @@ -58,7 +60,7 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_PHASE' { ext.args = ["--impute-reference-only-variants"].join(' ') - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chunk.replace(':','_')}_phase" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse1" } ext.suffix = "bcf" publishDir = [ enabled: false ] } @@ -69,7 +71,7 @@ process { } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_LIGATE' { - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chr}_ligate" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.ligate.glimpse1" } publishDir = [ enabled: false ] } @@ -89,6 +91,6 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_CONCAT' { ext.args = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ') - ext.prefix = { "${meta.id}_batch${meta.batch}.glimpse1" } + ext.prefix = { "${meta.id}.batch${meta.batch}.glimpse1" } } } diff --git a/conf/steps/imputation_glimpse2.config b/conf/steps/imputation_glimpse2.config index 1b5784b9..76ef02ce 100644 --- a/conf/steps/imputation_glimpse2.config +++ b/conf/steps/imputation_glimpse2.config @@ -18,7 +18,8 @@ process { } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_GLIMPSE2:GLIMPSE2_PHASE' { - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chunk.replace(':','_')}_glimpse2" } + cache = "lenient" + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse2" } ext.args = { "--keep-monomorphic-ref-sites" } ext.suffix = "bcf" publishDir = [ enabled: false ] @@ -30,7 +31,7 @@ process { } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_GLIMPSE2:GLIMPSE2_LIGATE' { - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chr}_ligate" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.ligate" } publishDir = [ enabled: false ] } @@ -51,6 +52,6 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE2:BCFTOOLS_CONCAT' { ext.args = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ') - ext.prefix = { "${meta.id}_batch${meta.batch}.glimpse2" } + ext.prefix = { "${meta.id}.batch${meta.batch}.glimpse2" } } } diff --git a/conf/steps/imputation_quilt.config b/conf/steps/imputation_quilt.config index 23457e71..acd2d2cc 100644 --- a/conf/steps/imputation_quilt.config +++ b/conf/steps/imputation_quilt.config @@ -23,14 +23,14 @@ process { // Impute quilt withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT:QUILT_QUILT' { ext.args = "--seed=${params.seed}" - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chr}_${meta.chunk}.impute" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.quilt" } publishDir = [enabled: false] } // Annotate quilt imputed VCFs withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT:BCFTOOLS_ANNOTATE' { ext.args = ["--set-id '%CHROM:%POS:%REF:%ALT'", "-Oz", "--write-index=tbi"].join(' ') - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chr}_${meta.chunk}.impute.annotate" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.quilt.annotate" } publishDir = [ enabled: false ] } @@ -45,6 +45,6 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_CONCAT' { ext.args = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ') - ext.prefix = { "${meta.id}_batch${meta.batch}.quilt" } + ext.prefix = { "${meta.id}.batch${meta.batch}.quilt" } } } diff --git a/conf/steps/imputation_stitch.config b/conf/steps/imputation_stitch.config index c84c34a7..172d2ba2 100644 --- a/conf/steps/imputation_stitch.config +++ b/conf/steps/imputation_stitch.config @@ -18,14 +18,15 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:GAWK' { ext.args2 = "'BEGIN { OFS=\"\\t\" } NR>1 { split(\$1, a, \"[:-_]\"); print a[1], \$2, \$3, \$4 }'" // Remove duplicates - ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chr}_posfile_stitch" } + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.posfile.stitch" } ext.suffix = "txt" publishDir = [enabled: false] tag = {"${meta.id} ${meta.chr}"} } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:STITCH' { - ext.prefix = { "${meta.id}_batch${meta.batch}.stitch" } + cache = "lenient" + ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.stitch" } } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:BCFTOOLS_INDEX' { @@ -44,6 +45,6 @@ process { withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_CONCAT' { ext.args = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ') - ext.prefix = { "${meta.id}_batch${meta.batch}.stitch" } + ext.prefix = { "${meta.id}.batch${meta.batch}.stitch" } } } diff --git a/conf/steps/panel_prep.config b/conf/steps/panel_prep.config index 3ab60861..6bed0f27 100644 --- a/conf/steps/panel_prep.config +++ b/conf/steps/panel_prep.config @@ -185,7 +185,7 @@ process { } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' { - ext.args = "--window-size 4" + ext.args = "--window-size 4000000" ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" } publishDir = [ path: { "${params.outdir}/prep_panel/chunks/glimpse1/" }, diff --git a/conf/steps/validation.config b/conf/steps/validation.config index 3a9b85cb..b5ca4fde 100644 --- a/conf/steps/validation.config +++ b/conf/steps/validation.config @@ -35,7 +35,7 @@ process { "-Aim", "-C alleles" ].join(' ') - ext.prefix = { "${meta.id}_truth.call" } + ext.prefix = { "${meta.id}.truth.call" } } withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_MERGE' { @@ -52,7 +52,7 @@ process { // Concatenate the truth set withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_TRUTH:.*' { - ext.prefix = { "${meta.id}.A-truth" } + ext.prefix = { "${meta.id}.batch${meta.batch}.truth" } publishDir = [ path: { "${params.outdir}/validation/concat" }, mode: params.publish_dir_mode, @@ -84,7 +84,7 @@ process { publishDir = [ path: { "${params.outdir}/validation/samples" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') ? null : filename} ] } diff --git a/conf/test.config b/conf/test.config index f5c7b8dd..6774be7b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -13,7 +13,7 @@ process { resourceLimits = [ cpus: 4, - memory: '15.GB', + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_all.config b/conf/test_all.config index c16d7904..7cd9054b 100644 --- a/conf/test_all.config +++ b/conf/test_all.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '10.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_batch.config b/conf/test_batch.config index b71a0385..3c823680 100644 --- a/conf/test_batch.config +++ b/conf/test_batch.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_dog.config b/conf/test_dog.config index 6ebc015e..f7a86f98 100644 --- a/conf/test_dog.config +++ b/conf/test_dog.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_full.config b/conf/test_full.config index fa1e3475..f4048ae4 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -36,8 +36,8 @@ params { // Panelprep optional args remove_samples = "NA12878,NA12891,NA12892" normalize = true - compute_freq = true - phase = true + compute_freq = false + phase = false // Impute tools tools = "glimpse1" diff --git a/conf/test_glimpse2.config b/conf/test_glimpse2.config index 1ea1e2f4..11562d33 100644 --- a/conf/test_glimpse2.config +++ b/conf/test_glimpse2.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_panelprep.config b/conf/test_panelprep.config index f62f2189..d85cbc90 100644 --- a/conf/test_panelprep.config +++ b/conf/test_panelprep.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_quilt.config b/conf/test_quilt.config index 40c2d31a..1f305de3 100644 --- a/conf/test_quilt.config +++ b/conf/test_quilt.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_sim.config b/conf/test_sim.config index 6eb0f1cb..e05362ea 100644 --- a/conf/test_sim.config +++ b/conf/test_sim.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_stitch.config b/conf/test_stitch.config index d9c50a14..8699253c 100644 --- a/conf/test_stitch.config +++ b/conf/test_stitch.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/conf/test_validate.config b/conf/test_validate.config index 254d808f..29d703da 100644 --- a/conf/test_validate.config +++ b/conf/test_validate.config @@ -12,8 +12,8 @@ process { resourceLimits = [ - cpus: 2, - memory: '2.GB', + cpus: 4, + memory: '4.GB', time: '1.h' ] } diff --git a/docs/usage.md b/docs/usage.md index 986a7e5f..3efc3d8d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -241,6 +241,18 @@ The required flags for this mode are: - `--remove_samples`: (optional) A comma-separated list of samples to remove from the reference during the normalization process. - `--compute_freq`: (optional) Whether the frequency (AC/AN field) for each variants needs to be computed or not (true/false). This can be the case if the frequency is absent from the reference panel or if individuals have been removed. +The panel will be chunked using the `GLIMPSE_CHUNKS` process. The size of the chunks can be optimized according to your needs (e.g. cluster resources, specie chromosomes size, ...) using the following config. The 4mb size (default value) is empirically determined to be a good value in humans (i.e. enough parallelization but not too much). + +```config title="panel.config" +withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' { + ext.args = "--window-size 4000000" +} + +withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' { + ext.args = "--window-mb 4" +} +``` + You can find an overview of the results produced by this steps in the [Output](output.md). ## Start with imputation `--steps impute` diff --git a/subworkflows/local/bam_impute_quilt/main.nf b/subworkflows/local/bam_impute_quilt/main.nf index 94c891aa..1f36cd8d 100644 --- a/subworkflows/local/bam_impute_quilt/main.nf +++ b/subworkflows/local/bam_impute_quilt/main.nf @@ -37,7 +37,7 @@ workflow BAM_IMPUTE_QUILT { .map { metaI, bam, bai, bamlist, metaPC, hap, legend, chr, start, end, ngen, buffer, gmap -> [ - metaI + [panel: metaPC.id, chr: metaPC.chr, chunk: start + "-" + end], + metaI + [panel: metaPC.id, chr: metaPC.chr, chunk: metaPC.chr + ":" + start + "-" + end], bam, bai, bamlist, hap, legend, chr, start, end, ngen, buffer, gmap ] } diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf index 64f90e95..23da802d 100644 --- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf @@ -275,6 +275,25 @@ workflow PIPELINE_INITIALISATION { .collect() .subscribe { log.info "The following contigs will be processed: ${it}" } + // Remove other contigs from panel and posfile files + ch_panel = ch_panel + .combine(ch_regions.collect{ it[0]["chr"]}.toList()) + .filter { meta, _vcf, _index, chrs -> + meta.chr in chrs + } + .map {meta, vcf, index, _chrs -> + [meta, vcf, index] + } + + ch_posfile = ch_posfile + .combine(ch_regions.collect{ it[0]["chr"]}.toList()) + .filter { meta, _vcf, _index, _hap, _legend, chrs -> + meta.chr in chrs + } + .map {meta, vcf, index, hap, legend, _chrs -> + [meta, vcf, index, hap, legend] + } + // Check that all input files have the correct index checkFileIndex(ch_input.mix(ch_input_truth, ch_ref_gen, ch_panel)) diff --git a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap index b4a9bd23..5a00a776 100644 --- a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap +++ b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap @@ -1,58 +1,6 @@ { "Phase vcf with regions, no map, no ref, no scaffold, sequential model": { "content": [ - { - "0": [ - [ - { - "id": "1000GP", - "chr": "chr21" - }, - "1000GP.vcf.gz:md5,4029303e3c083ebb2522fb5c8dc4b63a", - "1000GP.vcf.gz.csi:md5,c57057d136f6c859aac4e6ae28ec793b" - ], - [ - { - "id": "1000GP", - "chr": "chr22" - }, - "1000GP.vcf.gz:md5,23d09ba884eda7449702fece3f652d9d", - "1000GP.vcf.gz.csi:md5,281791c87517a6f3e83c3fd736ec704e" - ] - ], - "1": [ - "versions.yml:md5,529c03b8d921c72026e91d71c0321811", - "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6", - "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714", - "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b", - "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e" - ], - "vcf_tbi": [ - [ - { - "id": "1000GP", - "chr": "chr21" - }, - "1000GP.vcf.gz:md5,4029303e3c083ebb2522fb5c8dc4b63a", - "1000GP.vcf.gz.csi:md5,c57057d136f6c859aac4e6ae28ec793b" - ], - [ - { - "id": "1000GP", - "chr": "chr22" - }, - "1000GP.vcf.gz:md5,23d09ba884eda7449702fece3f652d9d", - "1000GP.vcf.gz.csi:md5,281791c87517a6f3e83c3fd736ec704e" - ] - ], - "versions": [ - "versions.yml:md5,529c03b8d921c72026e91d71c0321811", - "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6", - "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714", - "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b", - "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e" - ] - }, [ "versions.yml:md5,529c03b8d921c72026e91d71c0321811", "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6", @@ -84,74 +32,47 @@ ] ], "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-10T19:18:52.508986134" + "timestamp": "2024-11-12T14:46:00.916017807" }, "Phase vcf with regions, no map, no ref, no scaffold, recursive model": { "content": [ - { - "0": [ - [ - { - "id": "1000GP", - "chr": "chr21" - }, - "1000GP.vcf.gz:md5,d454c821a71b7c569540e381068fbe03", - "1000GP.vcf.gz.csi:md5,13e80ee9a038a715efd6f97befec28c6" - ], - [ - { - "id": "1000GP", - "chr": "chr22" - }, - "1000GP.vcf.gz:md5,68e488b81ea8ca52a52b20fec603bf3e", - "1000GP.vcf.gz.csi:md5,98037a25e4112f8a4df62eba96d08634" - ] - ], - "1": [ - "versions.yml:md5,529c03b8d921c72026e91d71c0321811", - "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6", - "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714", - "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b", - "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e" - ], - "vcf_tbi": [ - [ - { - "id": "1000GP", - "chr": "chr21" - }, - "1000GP.vcf.gz:md5,d454c821a71b7c569540e381068fbe03", - "1000GP.vcf.gz.csi:md5,13e80ee9a038a715efd6f97befec28c6" - ], - [ - { - "id": "1000GP", - "chr": "chr22" - }, - "1000GP.vcf.gz:md5,68e488b81ea8ca52a52b20fec603bf3e", - "1000GP.vcf.gz.csi:md5,98037a25e4112f8a4df62eba96d08634" - ] + [ + "versions.yml:md5,529c03b8d921c72026e91d71c0321811", + "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6", + "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714", + "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b", + "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e" + ], + [ + [ + { + "id": "1000GP", + "chr": "chr21" + }, + "1000GP.vcf.gz", + "1000GP.vcf.gz.csi" ], - "versions": [ - "versions.yml:md5,529c03b8d921c72026e91d71c0321811", - "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6", - "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714", - "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b", - "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e" + [ + { + "id": "1000GP", + "chr": "chr22" + }, + "1000GP.vcf.gz", + "1000GP.vcf.gz.csi" ] - }, + ], [ "VcfFile [chromosomes=[chr21], sampleCount=3196, variantCount=836, phased=true, phasedAutodetect=true]", "VcfFile [chromosomes=[chr22], sampleCount=3196, variantCount=903, phased=true, phasedAutodetect=true]" ] ], "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-10T19:18:20.407509527" + "timestamp": "2024-11-12T14:45:28.783070136" } } \ No newline at end of file diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap index d6084e40..5f1d9236 100644 --- a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap +++ b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap @@ -60,4 +60,4 @@ }, "timestamp": "2024-11-22T13:53:01.127637055" } -} \ No newline at end of file +} diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf index 34ea9e40..347d562a 100644 --- a/workflows/phaseimpute/main.nf +++ b/workflows/phaseimpute/main.nf @@ -42,23 +42,19 @@ include { VCF_SPLIT_BCFTOOLS } from '../../subworkflows/ include { BAM_GL_BCFTOOLS as GL_GLIMPSE1 } from '../../subworkflows/local/bam_gl_bcftools' include { VCF_IMPUTE_GLIMPSE1 } from '../../subworkflows/local/vcf_impute_glimpse1' include { VCF_CONCATENATE_BCFTOOLS as CONCAT_GLIMPSE1} from '../../subworkflows/local/vcf_concatenate_bcftools' -include { VCF_SPLIT_BCFTOOLS as SPLIT_GLIMPSE1 } from '../../subworkflows/local/vcf_split_bcftools' // GLIMPSE2 subworkflows include { BAM_IMPUTE_GLIMPSE2 } from '../../subworkflows/local/bam_impute_glimpse2' include { VCF_CONCATENATE_BCFTOOLS as CONCAT_GLIMPSE2} from '../../subworkflows/local/vcf_concatenate_bcftools' -include { VCF_SPLIT_BCFTOOLS as SPLIT_GLIMPSE2 } from '../../subworkflows/local/vcf_split_bcftools' // QUILT subworkflows include { VCF_CHUNK_GLIMPSE } from '../../subworkflows/local/vcf_chunk_glimpse' include { BAM_IMPUTE_QUILT } from '../../subworkflows/local/bam_impute_quilt' include { VCF_CONCATENATE_BCFTOOLS as CONCAT_QUILT } from '../../subworkflows/local/vcf_concatenate_bcftools' -include { VCF_SPLIT_BCFTOOLS as SPLIT_QUILT } from '../../subworkflows/local/vcf_split_bcftools' // STITCH subworkflows include { BAM_IMPUTE_STITCH } from '../../subworkflows/local/bam_impute_stitch' include { VCF_CONCATENATE_BCFTOOLS as CONCAT_STITCH } from '../../subworkflows/local/vcf_concatenate_bcftools' -include { VCF_SPLIT_BCFTOOLS as SPLIT_STITCH } from '../../subworkflows/local/vcf_split_bcftools' // Imputation stats include { BCFTOOLS_STATS as BCFTOOLS_STATS_TOOLS } from '../../modules/nf-core/bcftools/stats' @@ -391,7 +387,7 @@ workflow PHASEIMPUTE { // Export all files to csv exportCsv( ch_input_validate.map{ meta, file, index -> - [meta, [2:"imputation/${meta.tools}/concat", 3:"imputation/${meta.tools}/concat"], file, index] + [meta, [2:"imputation/${meta.tools}/samples/", 3:"imputation/${meta.tools}/samples/"], file, index] }, ["id", "tools"], "sample,tools,vcf,index", "impute.csv", "imputation/csv" diff --git a/workflows/phaseimpute/tests/main.nf.test b/workflows/phaseimpute/tests/main.nf.test index e23bcd44..6d9eeca1 100644 --- a/workflows/phaseimpute/tests/main.nf.test +++ b/workflows/phaseimpute/tests/main.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { .list() .collect { getRecursiveFileNames(it, outputDir) } .flatten(), - path("$outputDir/imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("$outputDir/imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz").vcf.header.getGenotypeSamples().sort() + path("$outputDir/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("$outputDir/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.header.getGenotypeSamples().sort() ).match() } ) @@ -51,8 +51,8 @@ nextflow_pipeline { .list() .collect { getRecursiveFileNames(it, outputDir) } .flatten(), - path("$outputDir/imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("$outputDir/imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort() + path("$outputDir/imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("$outputDir/imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort() ).match() } ) @@ -77,8 +77,8 @@ nextflow_pipeline { .list() .collect { getRecursiveFileNames(it, outputDir) } .flatten(), - path("$outputDir/imputation/quilt/concat/all_batch0.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("$outputDir/imputation/quilt/concat/all_batch0.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort() + path("$outputDir/imputation/quilt/concat/all.batch0.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("$outputDir/imputation/quilt/concat/all.batch0.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort() ).match() } ) @@ -104,8 +104,8 @@ nextflow_pipeline { .list() .collect { getRecursiveFileNames(it, outputDir) } .flatten(), - path("$outputDir/imputation/stitch/concat/all_batch0.stitch.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("$outputDir/imputation/stitch/concat/all_batch0.stitch.vcf.gz").vcf.header.getGenotypeSamples().sort() + path("$outputDir/imputation/stitch/concat/all.batch0.stitch.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("$outputDir/imputation/stitch/concat/all.batch0.stitch.vcf.gz").vcf.header.getGenotypeSamples().sort() ).match() } ) @@ -190,14 +190,14 @@ nextflow_pipeline { .list() .collect { getRecursiveFileNames(it, outputDir) } .flatten(), - path("${outputDir}/imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz").vcf.header.getGenotypeSamples().sort(), - path("${outputDir}/imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort(), - path("${outputDir}/imputation/stitch/concat/all_batch0.stitch.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/stitch/concat/all_batch0.stitch.vcf.gz").vcf.header.getGenotypeSamples().sort(), - path("${outputDir}/imputation/quilt/concat/all_batch0.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/quilt/concat/all_batch0.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort() + path("${outputDir}/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/stitch/concat/all.batch0.stitch.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/stitch/concat/all.batch0.stitch.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/quilt/concat/all.batch0.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/quilt/concat/all.batch0.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort() ).match() } ) @@ -274,14 +274,14 @@ nextflow_pipeline { .list() .collect { getRecursiveFileNames(it, outputDir) } .flatten(), - path("${outputDir}/imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort(), - path("${outputDir}/imputation/quilt/concat/all_batch0.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/quilt/concat/all_batch0.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort(), - path("${outputDir}/imputation/glimpse2/concat/all_batch1.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/glimpse2/concat/all_batch1.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort(), - path("${outputDir}/imputation/quilt/concat/all_batch1.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), - path("${outputDir}/imputation/quilt/concat/all_batch1.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/quilt/concat/all.batch0.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/quilt/concat/all.batch0.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/glimpse2/concat/all.batch1.glimpse2.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/glimpse2/concat/all.batch1.glimpse2.vcf.gz").vcf.header.getGenotypeSamples().sort(), + path("${outputDir}/imputation/quilt/concat/all.batch1.quilt.vcf.gz").vcf.summary.replaceAll(", phasedAutodetect=(false|true)", ""), + path("${outputDir}/imputation/quilt/concat/all.batch1.quilt.vcf.gz").vcf.header.getGenotypeSamples().sort(), path("${outputDir}/validation/") .list() .collect { getRecursiveFileNames(it, outputDir) } diff --git a/workflows/phaseimpute/tests/main.nf.test.snap b/workflows/phaseimpute/tests/main.nf.test.snap index ed71c96a..8553f530 100644 --- a/workflows/phaseimpute/tests/main.nf.test.snap +++ b/workflows/phaseimpute/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "Check test_stitch": { "content": [ [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", "imputation/csv/impute.csv", "imputation/stats/NA12878.stitch.bcftools_stats.txt", "imputation/stats/NA19401.stitch.bcftools_stats.txt", "imputation/stats/NA20359.stitch.bcftools_stats.txt", - "imputation/stitch/concat/all_batch0.stitch.vcf.gz", - "imputation/stitch/concat/all_batch0.stitch.vcf.gz.tbi", + "imputation/stitch/concat/all.batch0.stitch.vcf.gz", + "imputation/stitch/concat/all.batch0.stitch.vcf.gz.tbi", "imputation/stitch/samples/NA12878.vcf.gz", "imputation/stitch/samples/NA12878.vcf.gz.tbi", "imputation/stitch/samples/NA19401.vcf.gz", @@ -42,27 +42,27 @@ "simulation/samples/NA20359.depth_1x.bam.csi" ], [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", "imputation/csv/impute.csv", - "imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz", - "imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz", + "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz.tbi", "imputation/glimpse1/samples/NA12878.vcf.gz", "imputation/glimpse1/samples/NA12878.vcf.gz.tbi", "imputation/glimpse1/samples/NA19401.vcf.gz", "imputation/glimpse1/samples/NA19401.vcf.gz.tbi", "imputation/glimpse1/samples/NA20359.vcf.gz", "imputation/glimpse1/samples/NA20359.vcf.gz.tbi", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz.tbi", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi", "imputation/glimpse2/samples/NA12878.vcf.gz", "imputation/glimpse2/samples/NA12878.vcf.gz.tbi", "imputation/glimpse2/samples/NA19401.vcf.gz", "imputation/glimpse2/samples/NA19401.vcf.gz.tbi", "imputation/glimpse2/samples/NA20359.vcf.gz", "imputation/glimpse2/samples/NA20359.vcf.gz.tbi", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz.tbi", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi", "imputation/quilt/samples/NA12878.vcf.gz", "imputation/quilt/samples/NA12878.vcf.gz.tbi", "imputation/quilt/samples/NA19401.vcf.gz", @@ -81,8 +81,8 @@ "imputation/stats/NA20359.glimpse2.bcftools_stats.txt", "imputation/stats/NA20359.quilt.bcftools_stats.txt", "imputation/stats/NA20359.stitch.bcftools_stats.txt", - "imputation/stitch/concat/all_batch0.stitch.vcf.gz", - "imputation/stitch/concat/all_batch0.stitch.vcf.gz.tbi", + "imputation/stitch/concat/all.batch0.stitch.vcf.gz", + "imputation/stitch/concat/all.batch0.stitch.vcf.gz.tbi", "imputation/stitch/samples/NA12878.vcf.gz", "imputation/stitch/samples/NA12878.vcf.gz.tbi", "imputation/stitch/samples/NA19401.vcf.gz", @@ -115,8 +115,8 @@ "prep_panel/stats/1000GP.panel.bcftools_stats.txt" ], [ - "validation/concat/all.A-truth.vcf.gz", - "validation/concat/all.A-truth.vcf.gz.tbi", + "validation/concat/all.batch0.truth.vcf.gz", + "validation/concat/all.batch0.truth.vcf.gz.tbi", "validation/samples/NA12878.truth.vcf.gz", "validation/samples/NA12878.truth.vcf.gz.tbi", "validation/samples/NA19401.truth.vcf.gz", @@ -198,25 +198,25 @@ "Check test_batch": { "content": [ [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", - "imputation/batch/all.1.id.txt", - "imputation/batch/all.1.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", + "imputation/batch/all.batch1.id.txt", + "imputation/batch/all.batch1.noid.txt", "imputation/csv/impute.csv", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz.tbi", - "imputation/glimpse2/concat/all_batch1.glimpse2.vcf.gz", - "imputation/glimpse2/concat/all_batch1.glimpse2.vcf.gz.tbi", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi", + "imputation/glimpse2/concat/all.batch1.glimpse2.vcf.gz", + "imputation/glimpse2/concat/all.batch1.glimpse2.vcf.gz.tbi", "imputation/glimpse2/samples/NA12878.vcf.gz", "imputation/glimpse2/samples/NA12878.vcf.gz.tbi", "imputation/glimpse2/samples/NA19401.vcf.gz", "imputation/glimpse2/samples/NA19401.vcf.gz.tbi", "imputation/glimpse2/samples/NA20359.vcf.gz", "imputation/glimpse2/samples/NA20359.vcf.gz.tbi", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz.tbi", - "imputation/quilt/concat/all_batch1.quilt.vcf.gz", - "imputation/quilt/concat/all_batch1.quilt.vcf.gz.tbi", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi", + "imputation/quilt/concat/all.batch1.quilt.vcf.gz", + "imputation/quilt/concat/all.batch1.quilt.vcf.gz.tbi", "imputation/quilt/samples/NA12878.vcf.gz", "imputation/quilt/samples/NA12878.vcf.gz.tbi", "imputation/quilt/samples/NA19401.vcf.gz", @@ -276,11 +276,11 @@ "Check test_quilt": { "content": [ [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", "imputation/csv/impute.csv", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz.tbi", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi", "imputation/quilt/samples/NA12878.vcf.gz", "imputation/quilt/samples/NA12878.vcf.gz.tbi", "imputation/quilt/samples/NA19401.vcf.gz", @@ -302,7 +302,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-22T13:05:58.709941089" + "timestamp": "2024-11-23T19:41:54.261988901" }, "Check test_sim": { "content": [ @@ -357,11 +357,11 @@ "Check test_glimpse2": { "content": [ [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", "imputation/csv/impute.csv", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz.tbi", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi", "imputation/glimpse2/samples/NA12878.vcf.gz", "imputation/glimpse2/samples/NA12878.vcf.gz.tbi", "imputation/glimpse2/samples/NA19401.vcf.gz", @@ -388,11 +388,11 @@ "Check test": { "content": [ [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", "imputation/csv/impute.csv", - "imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz", - "imputation/glimpse1/concat/all_batch0.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz", + "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz.tbi", "imputation/glimpse1/samples/NA12878.vcf.gz", "imputation/glimpse1/samples/NA12878.vcf.gz.tbi", "imputation/glimpse1/samples/NA19401.vcf.gz", @@ -411,10 +411,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.1" }, - "timestamp": "2024-10-25T16:43:29.694533762" + "timestamp": "2024-11-23T19:36:03.277999895" }, "Check test_dog": { "content": [ @@ -442,19 +442,19 @@ "prep_panel/sites/658Dog_chr22_glimpse1_sites.vcf.gz.tbi" ], [ - "imputation/batch/all.0.id.txt", - "imputation/batch/all.0.noid.txt", + "imputation/batch/all.batch0.id.txt", + "imputation/batch/all.batch0.noid.txt", "imputation/csv/impute.csv", - "imputation/glimpse1/concat/dog_1735_batch0.glimpse1.vcf.gz", - "imputation/glimpse1/concat/dog_1735_batch0.glimpse1.vcf.gz.tbi", + "imputation/glimpse1/concat/dog_1735.batch0.glimpse1.vcf.gz", + "imputation/glimpse1/concat/dog_1735.batch0.glimpse1.vcf.gz.tbi", "imputation/glimpse1/samples/dog_1735.vcf.gz", "imputation/glimpse1/samples/dog_1735.vcf.gz.tbi", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz", - "imputation/glimpse2/concat/all_batch0.glimpse2.vcf.gz.tbi", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz", + "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi", "imputation/glimpse2/samples/dog_1735.vcf.gz", "imputation/glimpse2/samples/dog_1735.vcf.gz.tbi", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz", - "imputation/quilt/concat/all_batch0.quilt.vcf.gz.tbi", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz", + "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi", "imputation/quilt/samples/1735.vcf.gz", "imputation/quilt/samples/1735.vcf.gz.tbi", "imputation/stats/1735.quilt.bcftools_stats.txt",