From 6b5f48723c83e048a77db06b9d7dfef0bcf3042c Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 18:03:21 +0200 Subject: [PATCH 01/21] Migrate quilt to nf-test and swithc bamlist to auto generation inside the module --- modules/nf-core/quilt/quilt/main.nf | 10 +- .../nf-core/quilt/quilt/tests/main.nf.test | 129 ++++++++++++++++ .../quilt/quilt/tests/main.nf.test.snap | 83 ++++++++++ .../quilt/quilt/tests/quilt_default.config | 6 + .../quilt/quilt/tests/quilt_noseed.config | 6 + .../quilt/quilt/tests/quilt_optional.config | 6 + modules/nf-core/quilt/quilt/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/quilt/quilt/main.nf | 98 ------------ .../nf-core/quilt/quilt/nextflow.config | 18 --- tests/modules/nf-core/quilt/quilt/test.yml | 145 ------------------ 11 files changed, 237 insertions(+), 269 deletions(-) create mode 100644 modules/nf-core/quilt/quilt/tests/main.nf.test create mode 100644 modules/nf-core/quilt/quilt/tests/main.nf.test.snap create mode 100644 modules/nf-core/quilt/quilt/tests/quilt_default.config create mode 100644 modules/nf-core/quilt/quilt/tests/quilt_noseed.config create mode 100644 modules/nf-core/quilt/quilt/tests/quilt_optional.config create mode 100644 modules/nf-core/quilt/quilt/tests/tags.yml delete mode 100644 tests/modules/nf-core/quilt/quilt/main.nf delete mode 100644 tests/modules/nf-core/quilt/quilt/nextflow.config delete mode 100644 tests/modules/nf-core/quilt/quilt/test.yml diff --git a/modules/nf-core/quilt/quilt/main.nf b/modules/nf-core/quilt/quilt/main.nf index 3068ba7c962..982479b5c12 100644 --- a/modules/nf-core/quilt/quilt/main.nf +++ b/modules/nf-core/quilt/quilt/main.nf @@ -8,7 +8,7 @@ process QUILT_QUILT { 'biocontainers/r-quilt:1.0.5--r43h06b5641_0' }" input: - tuple val(meta), path(bams), path(bais), path(bamlist), path(reference_haplotype_file), path(reference_legend_file), val(chr), val(regions_start), val(regions_end), val(ngen), val(buffer), path(genetic_map_file) + tuple val(meta), path(bams), path(bais), path(reference_haplotype_file), path(reference_legend_file), val(chr), val(regions_start), val(regions_end), val(ngen), val(buffer), path(genetic_map_file) tuple val(meta2), path(posfile), path(phasefile) tuple val(meta3), path(fasta) @@ -27,18 +27,18 @@ process QUILT_QUILT { def prefix = task.ext.prefix ?: "${meta.id}" def extensions = bams.collect { it.extension } def extension = extensions.flatten().unique() - def list_command = extension == ["bam"] ? "--bamlist=${bamlist}" : - extension == ["cram"] ? "--cramlist=${bamlist} --reference=${fasta}" : "" + def list_command = extension == ["bam"] ? "--bamlist=" : + extension == ["cram"] ? "--reference=${fasta} --cramlist=" : "" def genetic_map_file_command = genetic_map_file ? "--genetic_map_file=${genetic_map_file}" : "" def posfile_command = posfile ? "--posfile=${posfile}" : "" def phasefile_command = phasefile ? "--phasefile=${phasefile}" : "" if (!(args ==~ /.*--seed.*/)) {args += " --seed=1"} """ - + printf "%s\\n" $bams | tr -d '[],' > all_files.txt QUILT.R \\ - $list_command \\ + ${list_command}all_files.txt \\ $genetic_map_file_command \\ $posfile_command \\ $phasefile_command \\ diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test new file mode 100644 index 00000000000..5e033014f5f --- /dev/null +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -0,0 +1,129 @@ +// Input data +def path = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/" +def bam = "[${path}NA12878.haplotagged.1.0.bam', checkIfExists: true), ${path}NA12878.ont.1.0.bam', checkIfExists: true), ${path}NA12878.illumina.1.0.bam', checkIfExists: true)]" +def bai = "[${path}NA12878.haplotagged.1.0.bam.bai', checkIfExists: true), ${path}NA12878.ont.1.0.bam.bai', checkIfExists: true),${path}NA12878.illumina.1.0.bam.bai', checkIfExists: true)]" + +// Input reference data +def reference_haplotype_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.hap.gz', checkIfExists: true)" +def reference_legend_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.legend.gz', checkIfExists: true)" +def genetic_map_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/CEU-chr20-final.b38.txt.gz', checkIfExists: true)" + +// Parameters +def chr = "'chr20'" +def regions_start = "2000001" +def regions_end = "2100000" +def ngen = "100" +def buffer = "10000" + + +// (optional) input truth data +def posfile = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.posfile.txt', checkIfExists: true)" +def phasefile = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.phasefile.txt', checkIfExists: true)" +def posfile_phasefile = "[[ id:'test', chr:'chr20' ], [$posfile], [$phasefile]]" +def fasta = "[[id:'test'], []]" + +// Input channel quilt +def ch_input = "[[ id:'test', chr:'chr20' ], $bam, $bai, [$reference_haplotype_file], [$reference_legend_file], $chr, $regions_start, $regions_end, $ngen, $buffer, [$genetic_map_file]]" + +nextflow_process { + + name "Test Process QUILT" + script "../main.nf" + process "QUILT_QUILT" + + tag "modules" + tag "modules_nfcore" + tag "quilt/quilt" + + test("QUILT") { + config ("./quilt_default.config") + when { + process { + """ + input[0] = $ch_input + input[1] = $posfile_phasefile + input[2] = $fasta + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("QUILT no optional files") { + config ("./quilt_default.config") + when { + process { + """ + posfile = [] + phasefile = [] + posfile_phasefile = [[id: null], posfile, phasefile] + genetic_map_file = [] + + ch_input = [ [ id:"test", chr:"chr20" ], bam, bai, bamlist, reference_haplotype_file, reference_legend_file, chr, regions_start, regions_end, ngen, buffer, genetic_map_file ] + + input[0] = ch_input + input[1] = posfile_phasefile + input[2] = fasta + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("QUILT optional output") { + config ("./quilt_optional.config") + when { + process { + """ + input[0] = ch_input + input[1] = posfile_phasefile + input[2] = fasta + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("QUILT no seed") { + config ("./quilt_noseed.config") + when { + process { + """ + input[0] = ch_input + input[1] = posfile_phasefile + input[2] = fasta + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap new file mode 100644 index 00000000000..e84fc868122 --- /dev/null +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -0,0 +1,83 @@ +{ + "QUILT": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ], + "1": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ], + "2": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ], + "plots": [ + + ], + "rdata": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "tbi": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ], + "vcf": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ], + "versions": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T18:01:49.782284167" + } +} \ No newline at end of file diff --git a/modules/nf-core/quilt/quilt/tests/quilt_default.config b/modules/nf-core/quilt/quilt/tests/quilt_default.config new file mode 100644 index 00000000000..87f87b9a61d --- /dev/null +++ b/modules/nf-core/quilt/quilt/tests/quilt_default.config @@ -0,0 +1,6 @@ +process { + cpus = 1 // More than 1 cpu may lead to different md5sum + withName: QUILT_QUILT { + ext.args = "--seed=1" + } +} diff --git a/modules/nf-core/quilt/quilt/tests/quilt_noseed.config b/modules/nf-core/quilt/quilt/tests/quilt_noseed.config new file mode 100644 index 00000000000..5ba34698c10 --- /dev/null +++ b/modules/nf-core/quilt/quilt/tests/quilt_noseed.config @@ -0,0 +1,6 @@ +process { + cpus = 1 // More than 1 cpu may lead to different md5sum + withName: QUILT { + ext.args = "" + } +} diff --git a/modules/nf-core/quilt/quilt/tests/quilt_optional.config b/modules/nf-core/quilt/quilt/tests/quilt_optional.config new file mode 100644 index 00000000000..4130d2a2259 --- /dev/null +++ b/modules/nf-core/quilt/quilt/tests/quilt_optional.config @@ -0,0 +1,6 @@ +process { + cpus = 1 // More than 1 cpu may lead to different md5sum + withName: QUILT { + ext.args = "--save_prepared_reference=TRUE --make_plots=TRUE --seed=1" + } +} diff --git a/modules/nf-core/quilt/quilt/tests/tags.yml b/modules/nf-core/quilt/quilt/tests/tags.yml new file mode 100644 index 00000000000..ac1b90920f2 --- /dev/null +++ b/modules/nf-core/quilt/quilt/tests/tags.yml @@ -0,0 +1,2 @@ +quilt/quilt: + - "modules/nf-core/quilt/quilt/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 22a6c7472b3..c1038eac90c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1609,9 +1609,6 @@ qcat: quast: - modules/nf-core/quast/** - tests/modules/nf-core/quast/** -quilt/quilt: - - modules/nf-core/quilt/quilt/** - - tests/modules/nf-core/quilt/quilt/** racon: - modules/nf-core/racon/** - tests/modules/nf-core/racon/** diff --git a/tests/modules/nf-core/quilt/quilt/main.nf b/tests/modules/nf-core/quilt/quilt/main.nf deleted file mode 100644 index 646ba8f6e35..00000000000 --- a/tests/modules/nf-core/quilt/quilt/main.nf +++ /dev/null @@ -1,98 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { QUILT_QUILT } from '../../../../../modules/nf-core/quilt/quilt/main.nf' -include { QUILT_QUILT as QUILT_OPTIONAL } from '../../../../../modules/nf-core/quilt/quilt/main.nf' -include { QUILT_QUILT as QUILT_NOSEED } from '../../../../../modules/nf-core/quilt/quilt/main.nf' - - - // input sequencing data (bam) - bam = [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/NA12878.haplotagged.1.0.bam', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/NA12878.ont.1.0.bam', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/NA12878.illumina.1.0.bam', checkIfExists: true) - ] - - bai = [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/NA12878.haplotagged.1.0.bam.bai', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/NA12878.ont.1.0.bam.bai', checkIfExists: true), - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/NA12878.illumina.1.0.bam.bai', checkIfExists: true) - ] - - bamlist = [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/bamlist.1.0.txt', checkIfExists: true) - ] - - bam_bai_bamlist = [ [ id:"test", chr:"chr20" ], bam, bai, bamlist ] - - // input reference data - - reference_haplotype_file = [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.hap.gz', checkIfExists: true) - ] - - reference_legend_file = [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.legend.gz', checkIfExists: true) - ] - - genetic_map_file = [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/CEU-chr20-final.b38.txt.gz', checkIfExists: true) - ] - - // parameters - - def chr = "chr20" - def regions_start = 2000001 - def regions_end = 2100000 - def ngen = 100 - def buffer = 10000 - - // input channel quilt - - ch_input = [ [ id:"test", chr:"chr20" ], bam, bai, bamlist, reference_haplotype_file, reference_legend_file, chr, regions_start, regions_end , ngen, buffer, genetic_map_file ] - - // (optional) input truth data - - posfile_phasefile = [ - [ id:'test', chr:"chr20" ], // meta map - [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.posfile.txt', checkIfExists: true) - ], - [ - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.phasefile.txt', checkIfExists: true) - ] - ] - - fasta = [[id:'test'], []] - - - -workflow test_quilt { - - QUILT_QUILT ( ch_input, posfile_phasefile, fasta ) -} - - -workflow test_quilt_no_optional_files { - - posfile = [] - phasefile = [] - posfile_phasefile = [[id: null], posfile, phasefile] - genetic_map_file = [] - - ch_input = [ [ id:"test", chr:"chr20" ], bam, bai, bamlist, reference_haplotype_file, reference_legend_file, chr, regions_start, regions_end, ngen, buffer, genetic_map_file ] - - - QUILT_QUILT ( ch_input, posfile_phasefile, fasta ) -} - -workflow test_quilt_optional_outputs { - - QUILT_OPTIONAL ( ch_input, posfile_phasefile, fasta ) -} - -workflow test_quilt_no_seed { - - QUILT_NOSEED ( ch_input, posfile_phasefile, fasta ) -} diff --git a/tests/modules/nf-core/quilt/quilt/nextflow.config b/tests/modules/nf-core/quilt/quilt/nextflow.config deleted file mode 100644 index 754998af134..00000000000 --- a/tests/modules/nf-core/quilt/quilt/nextflow.config +++ /dev/null @@ -1,18 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - cpus = 1 // More than 1 cpu may lead to different md5sum - - withName: QUILT_QUILT { - ext.args = "--seed=1" - } - - withName: QUILT_OPTIONAL { - ext.args = "--save_prepared_reference=TRUE --make_plots=TRUE --seed=1" - } - - withName: QUILT_NOSEED { - ext.args = "" - } - -} diff --git a/tests/modules/nf-core/quilt/quilt/test.yml b/tests/modules/nf-core/quilt/quilt/test.yml deleted file mode 100644 index d701986cf4b..00000000000 --- a/tests/modules/nf-core/quilt/quilt/test.yml +++ /dev/null @@ -1,145 +0,0 @@ -- name: quilt quilt test_quilt - command: nextflow run ./tests/modules/nf-core/quilt/quilt -entry test_quilt -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quilt/quilt/nextflow.config - tags: - - quilt/quilt - - quilt - files: - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz - md5sum: 81e23143117401f1f37a7c125ce37751 - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz.tbi - md5sum: 4607cdcb20599cbebd1ccf76d4dc56ae - - path: output/quilt/versions.yml - -- name: quilt quilt test_quilt_no_optional_files - command: nextflow run ./tests/modules/nf-core/quilt/quilt -entry test_quilt_no_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quilt/quilt/nextflow.config - tags: - - quilt/quilt - - quilt - files: - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz - md5sum: 65a415af7fa763422e628c2a418ab189 - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz.tbi - md5sum: 20d9e8cda03fc84482f3aa53a0c94fb6 - - path: output/quilt/versions.yml - -- name: quilt quilt test_quilt_optional_outputs - command: nextflow run ./tests/modules/nf-core/quilt/quilt -entry test_quilt_optional_outputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quilt/quilt/nextflow.config - tags: - - quilt/quilt - - quilt - files: - - path: output/quilt/RData/QUILT_prepared_reference.chr20.2000001.2100000.RData - md5sum: c2bbcf91085f33536fbaf094b4f0ea05 - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.1.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.1.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.1.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.1.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.2.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.2.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.2.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.2.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.3.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.3.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.3.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.3.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.4.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.4.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.4.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.4.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.5.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.5.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.5.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.5.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.6.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.6.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.6.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.6.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.7.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.7.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.7.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.7.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.8.0.truth.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.8.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.8.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878.chr20.2000001.2100000_igs.8.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.1.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.1.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.1.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.1.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.2.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.2.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.2.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.2.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.3.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.3.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.3.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.3.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.4.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.4.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.4.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.4.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.5.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.5.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.5.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.5.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.6.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.6.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.6.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.6.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.7.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.7.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.7.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.7.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.8.0.truth.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.8.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.8.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878HT.chr20.2000001.2100000_igs.8.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.1.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.1.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.1.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.1.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.2.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.2.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.2.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.2.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.3.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.3.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.3.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.3.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.4.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.4.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.4.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.4.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.5.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.5.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.5.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.5.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.6.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.6.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.6.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.6.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.7.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.7.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.7.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.7.it3.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.8.0.truth.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.8.it1.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.8.it2.gibbs.png - - path: output/quilt/plots/haps.NA12878ONT.chr20.2000001.2100000_igs.8.it3.gibbs.png - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz - md5sum: 251e93d85272bbfe5a3fc5b7b319b99c - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz.tbi - md5sum: 88d16933f2ac53058b7a5d5c849dc19a - - path: output/quilt/versions.yml - -- name: quilt quilt test_quilt_no_seed - command: nextflow run ./tests/modules/nf-core/quilt/quilt -entry test_quilt_no_seed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quilt/quilt/nextflow.config - tags: - - quilt/quilt - - quilt - files: - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz - md5sum: 81e23143117401f1f37a7c125ce37751 - - path: output/quilt/quilt.chr20.2000001.2100000.vcf.gz.tbi - md5sum: 4607cdcb20599cbebd1ccf76d4dc56ae - - path: output/quilt/versions.yml From 1f17d94be988d8bdc440778059fa86602e836ff6 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 18:09:17 +0200 Subject: [PATCH 02/21] Fix tests --- .../nf-core/quilt/quilt/tests/main.nf.test | 29 ++++++++----------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 5e033014f5f..03c387fdbd1 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -23,7 +23,9 @@ def posfile_phasefile = "[[ id:'test', chr:'chr20' ], [$posfile], [$phasefile]]" def fasta = "[[id:'test'], []]" // Input channel quilt -def ch_input = "[[ id:'test', chr:'chr20' ], $bam, $bai, [$reference_haplotype_file], [$reference_legend_file], $chr, $regions_start, $regions_end, $ngen, $buffer, [$genetic_map_file]]" +def ch_input = "[ id:'test', chr:'chr20' ], $bam, $bai, [$reference_haplotype_file], [$reference_legend_file], $chr, $regions_start, $regions_end, $ngen, $buffer" +def ch_input_gmap = "[$ch_input, [$genetic_map_file]]" +def ch_input_nogmap = "[$ch_input, []]" nextflow_process { @@ -40,7 +42,7 @@ nextflow_process { when { process { """ - input[0] = $ch_input + input[0] = $ch_input_gmap input[1] = $posfile_phasefile input[2] = $fasta """ @@ -61,15 +63,8 @@ nextflow_process { when { process { """ - posfile = [] - phasefile = [] - posfile_phasefile = [[id: null], posfile, phasefile] - genetic_map_file = [] - - ch_input = [ [ id:"test", chr:"chr20" ], bam, bai, bamlist, reference_haplotype_file, reference_legend_file, chr, regions_start, regions_end, ngen, buffer, genetic_map_file ] - - input[0] = ch_input - input[1] = posfile_phasefile + input[0] = ch_input_nogmap + input[1] = [[id: null], [], []] input[2] = fasta """ } @@ -89,9 +84,9 @@ nextflow_process { when { process { """ - input[0] = ch_input - input[1] = posfile_phasefile - input[2] = fasta + input[0] = $ch_input + input[1] = $posfile_phasefile + input[2] = $fasta """ } } @@ -110,9 +105,9 @@ nextflow_process { when { process { """ - input[0] = ch_input - input[1] = posfile_phasefile - input[2] = fasta + input[0] = $ch_input + input[1] = $posfile_phasefile + input[2] = $fasta """ } } From b25be83ba49dad257771d79ee1ee6bb5fdb1eb32 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 18:13:39 +0200 Subject: [PATCH 03/21] Fix test --- modules/nf-core/quilt/quilt/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 03c387fdbd1..bba873100fe 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -63,9 +63,9 @@ nextflow_process { when { process { """ - input[0] = ch_input_nogmap + input[0] = $ch_input_nogmap input[1] = [[id: null], [], []] - input[2] = fasta + input[2] = $fasta """ } } From cd3d1de3379daeb8438e55a5c6a6d5b1a0e2a1f7 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 18:16:36 +0200 Subject: [PATCH 04/21] Fix tests --- modules/nf-core/quilt/quilt/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index bba873100fe..127df5e13b9 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -84,7 +84,7 @@ nextflow_process { when { process { """ - input[0] = $ch_input + input[0] = $ch_input_gmap input[1] = $posfile_phasefile input[2] = $fasta """ @@ -105,7 +105,7 @@ nextflow_process { when { process { """ - input[0] = $ch_input + input[0] = $ch_input_gmap input[1] = $posfile_phasefile input[2] = $fasta """ From 01aa090c82eaa5fb84d9a92ce921aca885eaf95e Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 18:36:26 +0200 Subject: [PATCH 05/21] Add snap --- .../quilt/quilt/tests/main.nf.test.snap | 243 ++++++++++++++++++ 1 file changed, 243 insertions(+) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index e84fc868122..8a29eec6ca5 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -79,5 +79,248 @@ "nextflow": "23.10.1" }, "timestamp": "2024-04-22T18:01:49.782284167" + }, + "QUILT no seed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ], + "1": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ], + "2": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ], + "plots": [ + + ], + "rdata": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "tbi": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ], + "vcf": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ], + "versions": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T18:19:33.442049468" + }, + "QUILT no optional files": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,3fde483728ef2287416b2340c06aaf85" + ] + ], + "1": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,20d9e8cda03fc84482f3aa53a0c94fb6" + ] + ], + "2": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ], + "plots": [ + + ], + "rdata": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "tbi": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,20d9e8cda03fc84482f3aa53a0c94fb6" + ] + ], + "vcf": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,3fde483728ef2287416b2340c06aaf85" + ] + ], + "versions": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T18:18:28.787225185" + }, + "QUILT optional output": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ], + "1": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ], + "2": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ], + "plots": [ + + ], + "rdata": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + + ] + ] + ], + "tbi": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ], + "vcf": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ], + "versions": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T18:19:03.233474173" } } \ No newline at end of file From 7bfc5b0cd59d63c7005847cd158cf2dbe21ca5c3 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 21:56:17 +0200 Subject: [PATCH 06/21] Update license --- modules/nf-core/quilt/quilt/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/quilt/quilt/meta.yml b/modules/nf-core/quilt/quilt/meta.yml index 34c67a79db7..02d418d3cf2 100644 --- a/modules/nf-core/quilt/quilt/meta.yml +++ b/modules/nf-core/quilt/quilt/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/rwdavies/quilt" tool_dev_url: "https://github.com/rwdavies/quilt" doi: "10.1038/s41588-021-00877-0" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map From 5e3f8129c8b99a094d4af895e3bb8c810b840fe7 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 21:56:27 +0200 Subject: [PATCH 07/21] Add quilt tag --- modules/nf-core/quilt/quilt/tests/main.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 127df5e13b9..1de483ecd39 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -36,6 +36,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "quilt/quilt" + tag "quilt" test("QUILT") { config ("./quilt_default.config") From 6c1215247d314731ce5d43da3069718980b8c6af Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 22:07:59 +0200 Subject: [PATCH 08/21] Specify build hash for conda environment --- modules/nf-core/glimpse2/concordance/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/glimpse2/concordance/environment.yml b/modules/nf-core/glimpse2/concordance/environment.yml index c3ad98fbf17..9d5304165e0 100644 --- a/modules/nf-core/glimpse2/concordance/environment.yml +++ b/modules/nf-core/glimpse2/concordance/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::glimpse-bio=2.0.0 + - bioconda::glimpse-bio=2.0.0=r43h06b5641_0 From 806a7d9bcf92c5105448056a3d0da5c96b9f509b Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 22:21:17 +0200 Subject: [PATCH 09/21] Specify build hash for conda environment --- modules/nf-core/quilt/quilt/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/quilt/quilt/environment.yml b/modules/nf-core/quilt/quilt/environment.yml index 9872e81955e..160ac591592 100644 --- a/modules/nf-core/quilt/quilt/environment.yml +++ b/modules/nf-core/quilt/quilt/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::r-quilt=1.0.5 + - bioconda::r-quilt=1.0.5=r43h06b5641_0 From 9d46af35c33c6fe7105e999af6fdf828b10ace5a Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 22:21:52 +0200 Subject: [PATCH 10/21] Undo commit --- modules/nf-core/glimpse2/concordance/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/glimpse2/concordance/environment.yml b/modules/nf-core/glimpse2/concordance/environment.yml index 9d5304165e0..c3ad98fbf17 100644 --- a/modules/nf-core/glimpse2/concordance/environment.yml +++ b/modules/nf-core/glimpse2/concordance/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::glimpse-bio=2.0.0=r43h06b5641_0 + - bioconda::glimpse-bio=2.0.0 From 2854b34a15c6ea2465cb2de56edd41020b0d3306 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 23:48:46 +0200 Subject: [PATCH 11/21] Update nf-test snapshot --- modules/nf-core/quilt/quilt/tests/main.nf.test | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 1de483ecd39..43b7a388081 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -53,7 +53,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out.vcf).match("quilt_vcf") }, + { assert snapshot(process.out.tbi).match("quilt_tbi") }, + { assert file(process.out.versions[0]).exists()} ) } @@ -74,7 +76,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out.vcf).match("quilt_noopt_vcf") }, + { assert snapshot(process.out.tbi).match("quilt_noopt_tbi") }, + { assert file(process.out.versions[0]).exists()} ) } @@ -95,7 +99,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out.vcf).match("quilt_opt_vcf") }, + { assert snapshot(process.out.tbi).match("quilt_opt_tbi") }, + { assert snapshot(process.out.plots).match("quilt_opt_plots") }, + { assert snapshot(process.out.rdata).match("quilt_opt_rdata") }, + { assert file(process.out.versions[0]).exists() } ) } @@ -116,7 +124,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out.vcf).match("quilt_noseed_vcf") }, + { assert snapshot(process.out.tbi).match("quilt_noseed_tbi") }, + { assert file(process.out.versions[0]).exists()} ) } From c3784fe1b3b67e65850a2f4ebdfc722c8155504b Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 23:49:04 +0200 Subject: [PATCH 12/21] Fix config name --- modules/nf-core/quilt/quilt/tests/quilt_noseed.config | 2 +- modules/nf-core/quilt/quilt/tests/quilt_optional.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/quilt_noseed.config b/modules/nf-core/quilt/quilt/tests/quilt_noseed.config index 5ba34698c10..e9f81a34f96 100644 --- a/modules/nf-core/quilt/quilt/tests/quilt_noseed.config +++ b/modules/nf-core/quilt/quilt/tests/quilt_noseed.config @@ -1,6 +1,6 @@ process { cpus = 1 // More than 1 cpu may lead to different md5sum - withName: QUILT { + withName: QUILT_QUILT { ext.args = "" } } diff --git a/modules/nf-core/quilt/quilt/tests/quilt_optional.config b/modules/nf-core/quilt/quilt/tests/quilt_optional.config index 4130d2a2259..cfbd1353c43 100644 --- a/modules/nf-core/quilt/quilt/tests/quilt_optional.config +++ b/modules/nf-core/quilt/quilt/tests/quilt_optional.config @@ -1,6 +1,6 @@ process { cpus = 1 // More than 1 cpu may lead to different md5sum - withName: QUILT { + withName: QUILT_QUILT { ext.args = "--save_prepared_reference=TRUE --make_plots=TRUE --seed=1" } } From 694c1fd403361fcf42e71e434ae0432a0ef591bc Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 22 Apr 2024 23:52:36 +0200 Subject: [PATCH 13/21] Update snapshot --- .../quilt/quilt/tests/main.nf.test.snap | 531 ++++++++---------- 1 file changed, 243 insertions(+), 288 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index 8a29eec6ca5..75da249db5d 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -1,326 +1,281 @@ { - "QUILT": { + "quilt_vcf": { "content": [ - { - "0": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" - ] - ], - "1": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" - ] - ], - "2": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "3": [ - - ], - "4": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" - ], - "plots": [ - - ], - "rdata": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "tbi": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" - ] - ], - "vcf": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" - ] - ], - "versions": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" ] - } + ] ], "meta": { 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- "1": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" - ] - ], - "2": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "3": [ - - ], - "4": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" - ], - "plots": [ - - ], - "rdata": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "tbi": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" - ] - ], - "vcf": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" - ] - ], - "versions": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" ] - } + ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-22T18:19:33.442049468" + "timestamp": "2024-04-22T23:27:09.731885213" }, - "QUILT no optional files": { + "quilt_opt_rdata": { "content": [ - { - "0": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,3fde483728ef2287416b2340c06aaf85" - ] - ], - "1": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,20d9e8cda03fc84482f3aa53a0c94fb6" - ] - ], - "2": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "3": [ - - ], - "4": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" - ], - "plots": [ - - ], - "rdata": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "tbi": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,20d9e8cda03fc84482f3aa53a0c94fb6" - ] - ], - "vcf": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,3fde483728ef2287416b2340c06aaf85" + "QUILT_prepared_reference.chr20.2000001.2100000.RData:md5,c2bbcf91085f33536fbaf094b4f0ea05" ] - ], - "versions": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" ] - } + ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-22T18:18:28.787225185" + "timestamp": "2024-04-22T23:27:11.359674847" }, - "QUILT optional output": { + "quilt_noseed_tbi": { "content": [ - { - "0": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" - ] - ], - "1": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" - ] - ], - "2": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "3": [ - - ], - "4": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" - ], - "plots": [ - - ], - "rdata": [ - [ - { - "id": "test", - "chr": "chr20" - }, - [ - - ] - ] - ], - "tbi": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" - ] - ], - "vcf": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" - ] - ], - "versions": [ - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T23:27:49.582449342" + }, + "quilt_noopt_tbi": { + "content": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,20d9e8cda03fc84482f3aa53a0c94fb6" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T23:26:25.94907551" + }, + "quilt_opt_vcf": { + "content": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,8352fbcabdd102a8ba2c4490e0834287" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T23:27:09.323762188" + }, + "quilt_noseed_vcf": { + "content": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T23:27:47.856247585" + }, + "quilt_tbi": { + "content": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,4607cdcb20599cbebd1ccf76d4dc56ae" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T23:26:05.085319655" + }, + "quilt_noopt_vcf": { + "content": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,3fde483728ef2287416b2340c06aaf85" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-22T23:26:25.825599064" + }, + "quilt_opt_tbi": { + "content": [ + [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,88d16933f2ac53058b7a5d5c849dc19a" ] - } + ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-22T18:19:03.233474173" + "timestamp": "2024-04-22T23:27:09.524895119" } } \ No newline at end of file From 2a88716cd10eb675bb23c0606c9a7fe30576bf7a Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 11:48:35 +0200 Subject: [PATCH 14/21] Update meta.yml --- modules/nf-core/quilt/quilt/meta.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/quilt/quilt/meta.yml b/modules/nf-core/quilt/quilt/meta.yml index 02d418d3cf2..412d1bc66d1 100644 --- a/modules/nf-core/quilt/quilt/meta.yml +++ b/modules/nf-core/quilt/quilt/meta.yml @@ -28,10 +28,6 @@ input: type: file description: (Mandatory) BAM/CRAM index files pattern: "*.{bai}" - - bamlist: - type: file - description: (Mandatory) "Path to file with bam file locations. File is one row per entry, path to bam files. Bam index files should exist in same directory as for each bam, suffixed either .bam.bai or .bai. - pattern: "*.{txt}" - reference_haplotype_file: type: file description: (Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1) @@ -99,9 +95,12 @@ output: type: file description: TBI file of the VCF. pattern: "*.{vcf.gz.tbi}" - - RData: + - rdata: type: directory description: Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE). + - plots: + type: directory + description: Optional directory path to save plots. authors: - "@atrigila" maintainers: From 6b89cb1fac84cc98075479825ad49122328b7554 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 11:50:07 +0200 Subject: [PATCH 15/21] Add r-base to environment --- modules/nf-core/quilt/quilt/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/quilt/quilt/environment.yml b/modules/nf-core/quilt/quilt/environment.yml index 160ac591592..a2161a6515d 100644 --- a/modules/nf-core/quilt/quilt/environment.yml +++ b/modules/nf-core/quilt/quilt/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::r-quilt=1.0.5=r43h06b5641_0 + - r-base=4.3.1 From 9ffc43026ee4dcae2e40e9e4a598031e341bcdf1 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 11:51:06 +0200 Subject: [PATCH 16/21] Update snapshot generation --- .../nf-core/quilt/quilt/tests/main.nf.test | 20 ++++++------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 43b7a388081..18a173780b3 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -53,9 +53,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.vcf).match("quilt_vcf") }, - { assert snapshot(process.out.tbi).match("quilt_tbi") }, - { assert file(process.out.versions[0]).exists()} + { assert snapshot(process.out).match() } ) } @@ -76,9 +74,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.vcf).match("quilt_noopt_vcf") }, - { assert snapshot(process.out.tbi).match("quilt_noopt_tbi") }, - { assert file(process.out.versions[0]).exists()} + { assert snapshot(process.out).match() } ) } @@ -99,11 +95,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.vcf).match("quilt_opt_vcf") }, - { assert snapshot(process.out.tbi).match("quilt_opt_tbi") }, - { assert snapshot(process.out.plots).match("quilt_opt_plots") }, - { assert snapshot(process.out.rdata).match("quilt_opt_rdata") }, - { assert file(process.out.versions[0]).exists() } + { assert process.success }, + { assert snapshot(process.out).match() } ) } @@ -124,9 +117,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.vcf).match("quilt_noseed_vcf") }, - { assert snapshot(process.out.tbi).match("quilt_noseed_tbi") }, - { assert file(process.out.versions[0]).exists()} + { assert process.success }, + { assert snapshot(process.out).match() } ) } From f6fec806a33ad49d770ad714ed4064b8f3202593 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 11:55:23 +0200 Subject: [PATCH 17/21] Update meta.yml --- modules/nf-core/quilt/quilt/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/quilt/quilt/meta.yml b/modules/nf-core/quilt/quilt/meta.yml index 412d1bc66d1..e4653983217 100644 --- a/modules/nf-core/quilt/quilt/meta.yml +++ b/modules/nf-core/quilt/quilt/meta.yml @@ -99,8 +99,8 @@ output: type: directory description: Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE). - plots: - type: directory - description: Optional directory path to save plots. + type: directory + description: Optional directory path to save plots. authors: - "@atrigila" maintainers: From ed206223cbc32620926887e77807413cf741e31e Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 12:01:09 +0200 Subject: [PATCH 18/21] Update snap --- .../quilt/quilt/tests/main.nf.test.snap | 737 ++++++++++++------ 1 file changed, 494 insertions(+), 243 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index 75da249db5d..a227b401057 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -1,281 +1,532 @@ { - "quilt_vcf": { + "QUILT": { "content": [ - [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,32f539c80971e2e8e0c31870be094a25" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - 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+ ], + "rdata": [ + [ + { + "id": "test", + "chr": "chr20" + }, + [ + "QUILT_prepared_reference.chr20.2000001.2100000.RData:md5,c2bbcf91085f33536fbaf094b4f0ea05" + ] + ] + ], + "tbi": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,88d16933f2ac53058b7a5d5c849dc19a" + ] + ], + "vcf": [ + [ + { + "id": "test", + "chr": "chr20" + }, + "quilt.chr20.2000001.2100000.vcf.gz:md5,8352fbcabdd102a8ba2c4490e0834287" + ] + ], + "versions": [ + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" ] - ] + } ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-22T23:27:09.524895119" + "timestamp": "2024-04-23T12:00:05.735793393" } } \ No newline at end of file From f94728828c2f379842a41dd736cd1850627bdc19 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 16:45:24 +0200 Subject: [PATCH 19/21] Update snap --- .../nf-core/quilt/quilt/tests/main.nf.test | 11 +- .../quilt/quilt/tests/main.nf.test.snap | 413 ++++++------------ 2 files changed, 142 insertions(+), 282 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 18a173780b3..9a833d5265c 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -93,10 +93,16 @@ nextflow_process { } then { + def dir = new File(process.out.plots[0][1]) + def list = [] + dir.eachFileRecurse { file -> list << file.getName() } assertAll( { assert process.success }, - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(list).match("plots") }, + { assert snapshot( + process.out.vcf + process.out.tbi + + process.out.rdata + process.out.versions + ).match() } ) } @@ -116,7 +122,6 @@ nextflow_process { then { assertAll( - { assert process.success }, { assert process.success }, { assert snapshot(process.out).match() } ) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index a227b401057..3eaead39a92 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -78,7 +78,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T11:58:59.137414973" + "timestamp": "2024-04-23T16:42:42.340060096" }, "QUILT no seed": { "content": [ @@ -159,7 +159,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T12:00:38.413309308" + "timestamp": "2024-04-23T16:44:16.093955491" }, "QUILT no optional files": { "content": [ @@ -240,293 +240,148 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T11:59:18.714678928" + "timestamp": "2024-04-23T16:43:03.398802044" }, "QUILT optional output": { "content": [ - { - "0": [ - [ - { - "id": "test", - "chr": "chr20" - }, - "quilt.chr20.2000001.2100000.vcf.gz:md5,8352fbcabdd102a8ba2c4490e0834287" - ] - ], - "1": [ - [ - { - "id": "test", - "chr": 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], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T12:00:05.735793393" + "timestamp": "2024-04-23T16:43:45.507954653" } } \ No newline at end of file From 6b691ec83c17b2352f698e9a15d605f29bca0957 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 17:13:24 +0200 Subject: [PATCH 20/21] Force sorting --- modules/nf-core/quilt/quilt/tests/main.nf.test | 2 +- modules/nf-core/quilt/quilt/tests/main.nf.test.snap | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 9a833d5265c..35c5e576d02 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -98,7 +98,7 @@ nextflow_process { dir.eachFileRecurse { file -> list << file.getName() } assertAll( { assert process.success }, - { assert snapshot(list).match("plots") }, + { assert snapshot(list.sort()).match("plots") }, { assert snapshot( process.out.vcf + process.out.tbi + process.out.rdata + process.out.versions diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index 3eaead39a92..6ade7b8473a 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -78,7 +78,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T16:42:42.340060096" + "timestamp": "2024-04-23T17:10:53.023853874" }, "QUILT no seed": { "content": [ @@ -159,7 +159,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T16:44:16.093955491" + "timestamp": "2024-04-23T17:12:27.743495187" }, "QUILT no optional files": { "content": [ @@ -240,7 +240,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T16:43:03.398802044" + "timestamp": "2024-04-23T17:11:12.657951821" }, "QUILT optional output": { "content": [ @@ -275,7 +275,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T16:43:46.02397462" + "timestamp": "2024-04-23T17:11:56.27616283" }, "plots": { "content": [ @@ -382,6 +382,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T16:43:45.507954653" + "timestamp": "2024-04-23T17:11:55.826380953" } } \ No newline at end of file From bd28eeddce5f7ffaa35b94a73d4c0418783c01b7 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 17:30:27 +0200 Subject: [PATCH 21/21] Update snapshot --- .../nf-core/quilt/quilt/tests/main.nf.test | 2 +- .../quilt/quilt/tests/main.nf.test.snap | 41 +++++++------------ 2 files changed, 16 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test b/modules/nf-core/quilt/quilt/tests/main.nf.test index 35c5e576d02..2d80516df52 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test @@ -98,9 +98,9 @@ nextflow_process { dir.eachFileRecurse { file -> list << file.getName() } assertAll( { assert process.success }, - { assert snapshot(list.sort()).match("plots") }, { assert snapshot( process.out.vcf + process.out.tbi + + list.sort() + process.out.rdata + process.out.versions ).match() } ) diff --git a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap index 6ade7b8473a..191b519a53d 100644 --- a/modules/nf-core/quilt/quilt/tests/main.nf.test.snap +++ b/modules/nf-core/quilt/quilt/tests/main.nf.test.snap @@ -78,7 +78,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T17:10:53.023853874" + "timestamp": "2024-04-23T17:27:54.607934432" }, "QUILT no seed": { "content": [ @@ -159,7 +159,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T17:12:27.743495187" + "timestamp": "2024-04-23T17:29:31.357244889" }, "QUILT no optional files": { "content": [ @@ -240,7 +240,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T17:11:12.657951821" + "timestamp": "2024-04-23T17:28:16.39358682" }, "QUILT optional output": { "content": [ @@ -259,27 +259,6 @@ }, "quilt.chr20.2000001.2100000.vcf.gz.tbi:md5,88d16933f2ac53058b7a5d5c849dc19a" ], - [ - { - "id": "test", - "chr": "chr20" - }, - [ - "QUILT_prepared_reference.chr20.2000001.2100000.RData:md5,c2bbcf91085f33536fbaf094b4f0ea05" - ] - ], - "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-04-23T17:11:56.27616283" - }, - "plots": { - "content": [ - [ "haps.NA12878.chr20.2000001.2100000_igs.1.0.truth.png", "haps.NA12878.chr20.2000001.2100000_igs.1.it1.gibbs.png", "haps.NA12878.chr20.2000001.2100000_igs.1.it2.gibbs.png", @@ -375,13 +354,23 @@ "haps.NA12878ONT.chr20.2000001.2100000_igs.8.0.truth.png", "haps.NA12878ONT.chr20.2000001.2100000_igs.8.it1.gibbs.png", "haps.NA12878ONT.chr20.2000001.2100000_igs.8.it2.gibbs.png", - "haps.NA12878ONT.chr20.2000001.2100000_igs.8.it3.gibbs.png" + "haps.NA12878ONT.chr20.2000001.2100000_igs.8.it3.gibbs.png", + [ + { + "id": "test", + "chr": "chr20" + }, + [ + "QUILT_prepared_reference.chr20.2000001.2100000.RData:md5,c2bbcf91085f33536fbaf094b4f0ea05" + ] + ], + "versions.yml:md5,6d07cd60389ff6981a44004872bd16b7" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-04-23T17:11:55.826380953" + "timestamp": "2024-04-23T17:28:59.999377862" } } \ No newline at end of file