From 8afa912ec913c5f6dda3dcfee650da1fd4cab558 Mon Sep 17 00:00:00 2001 From: FernandoDuarteF <123090819+FernandoDuarteF@users.noreply.github.com> Date: Fri, 6 Sep 2024 18:06:42 +0100 Subject: [PATCH] Added nf-test for quast (#6554) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added nf-test for quast * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Tests for each optional input and removed pytest * Removed "ref, nogff" test --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --- modules/nf-core/quast/tests/main.nf.test | 105 ++++++ modules/nf-core/quast/tests/main.nf.test.snap | 331 ++++++++++++++++++ modules/nf-core/quast/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/quast/main.nf | 40 --- tests/modules/nf-core/quast/nextflow.config | 5 - tests/modules/nf-core/quast/test.yml | 233 ------------ 7 files changed, 438 insertions(+), 281 deletions(-) create mode 100644 modules/nf-core/quast/tests/main.nf.test create mode 100644 modules/nf-core/quast/tests/main.nf.test.snap create mode 100644 modules/nf-core/quast/tests/tags.yml delete mode 100644 tests/modules/nf-core/quast/main.nf delete mode 100644 tests/modules/nf-core/quast/nextflow.config delete mode 100644 tests/modules/nf-core/quast/test.yml diff --git a/modules/nf-core/quast/tests/main.nf.test b/modules/nf-core/quast/tests/main.nf.test new file mode 100644 index 00000000000..44655a526ac --- /dev/null +++ b/modules/nf-core/quast/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_process { + + name "Test Process QUAST" + script "../main.nf" + process "QUAST" + + tag "modules" + tag "modules_nfcore" + tag "quast" + + test("sarscov2 - ref") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) + ] + input[1] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.results[0][1]).list().size() == 15 }, + { assert snapshot( + process.out.tsv, + process.out.misassemblies, + process.out.unaligned, + process.out.versions, + ).match() } + ) + } + } + + test("sarscov2 - noref") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.results[0][1]).list().size() == 12 }, + { assert snapshot( + process.out.tsv, + process.out.versions, + ).match() } + ) + } + } + + + test("sarscov2 - all - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id: 'test1' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) + ] + input[1] = [ + [ id: 'test1' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id: 'test1' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/quast/tests/main.nf.test.snap b/modules/nf-core/quast/tests/main.nf.test.snap new file mode 100644 index 00000000000..f408a299c93 --- /dev/null +++ b/modules/nf-core/quast/tests/main.nf.test.snap @@ -0,0 +1,331 @@ +{ + "sarscov2 - ref, gff": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,1fc09ef5115692ed558cb31482bf3db0" + ] + ], + [ + [ + { + "id": "test" + }, + "test_misassemblies.tsv:md5,b2c977af2f6e07603e0a0f4d1e32d058" + ] + ], + [ + [ + { + "id": "test" + }, + "test_unaligned.tsv:md5,a3a36c1d206f89d12af74cef0c412f94" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T13:13:45.436004" + }, + "sarscov2 - noref, nogff": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,6c4891c111a46ed20d5e3062b71aa390" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T13:13:50.435479" + }, + "sarscov2 - all - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test1" + }, + [ + [ + "NAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "Nx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "gc.icarus.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "all_alignments_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.mis_contigs.info:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stderr:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stdout:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.unaligned.info:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "transcriptome.coords:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords.filtered:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords_tmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.sf:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.unaligned:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.used_snps:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "misassemblies_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.mis_contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "features_cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "features_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome_gaps.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "icarus.html:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "alignment_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "contig_size_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "quast.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + { + "id": "test1" + }, + "test1.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test1" + }, + "test1_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test1" + }, + "test1_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test1" + }, + "test1_unaligned.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ], + "misassemblies": [ + [ + { + "id": "test1" + }, + "test1_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "results": [ + [ + { + "id": "test1" + }, + [ + [ + "NAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "Nx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "gc.icarus.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "all_alignments_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.mis_contigs.info:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stderr:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stdout:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.unaligned.info:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "transcriptome.coords:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords.filtered:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords_tmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.sf:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.unaligned:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.used_snps:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "misassemblies_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.mis_contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "features_cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "features_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome_gaps.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "icarus.html:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "alignment_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "contig_size_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "quast.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "transcriptome": [ + [ + { + "id": "test1" + }, + "test1_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tsv": [ + [ + { + "id": "test1" + }, + "test1.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "unaligned": [ + [ + { + "id": "test1" + }, + "test1_unaligned.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T13:13:54.219263" + }, + "sarscov2 - ref": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,1fc09ef5115692ed558cb31482bf3db0" + ] + ], + [ + [ + { + "id": "test" + }, + "test_misassemblies.tsv:md5,b2c977af2f6e07603e0a0f4d1e32d058" + ] + ], + [ + [ + { + "id": "test" + }, + "test_unaligned.tsv:md5,a3a36c1d206f89d12af74cef0c412f94" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:58:43.030275" + }, + "sarscov2 - noref": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,6c4891c111a46ed20d5e3062b71aa390" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:58:58.400864" + } +} \ No newline at end of file diff --git a/modules/nf-core/quast/tests/tags.yml b/modules/nf-core/quast/tests/tags.yml new file mode 100644 index 00000000000..2bd72f4c0ab --- /dev/null +++ b/modules/nf-core/quast/tests/tags.yml @@ -0,0 +1,2 @@ +quast: + - modules/nf-core/quast/** diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e8273e4aa4c..f286ae2c2a4 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -575,9 +575,6 @@ purgedups/purgedups: pydamage/filter: - modules/nf-core/pydamage/filter/** - tests/modules/nf-core/pydamage/filter/** -quast: - - modules/nf-core/quast/** - - tests/modules/nf-core/quast/** raxmlng: - modules/nf-core/raxmlng/** - tests/modules/nf-core/raxmlng/** diff --git a/tests/modules/nf-core/quast/main.nf b/tests/modules/nf-core/quast/main.nf deleted file mode 100644 index 08c03106ee8..00000000000 --- a/tests/modules/nf-core/quast/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { QUAST as QUAST_REF } from '../../../../modules/nf-core/quast/main.nf' -include { QUAST as QUAST_NOREF_NOGFF } from '../../../../modules/nf-core/quast/main.nf' -include { QUAST as QUAST_NOGFF } from '../../../../modules/nf-core/quast/main.nf' -include { QUAST as QUAST_NOREF } from '../../../../modules/nf-core/quast/main.nf' - -workflow test_quast_ref { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] - gff = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)] - - QUAST_REF ( consensus, fasta, gff ) -} - -workflow test_quast_noref_nogff { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[:],[]] - gff = [[:],[]] - - QUAST_NOREF_NOGFF ( consensus, fasta, gff ) -} - -workflow test_quast_nogff { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] - gff = [[:],[]] - - QUAST_NOGFF ( consensus, fasta, gff ) -} - -workflow test_quast_noref { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[:],[]] - gff = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)] - - QUAST_NOREF ( consensus, fasta, gff ) -} diff --git a/tests/modules/nf-core/quast/nextflow.config b/tests/modules/nf-core/quast/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/quast/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/quast/test.yml b/tests/modules/nf-core/quast/test.yml deleted file mode 100644 index 54fddcd38b8..00000000000 --- a/tests/modules/nf-core/quast/test.yml +++ /dev/null @@ -1,233 +0,0 @@ -- name: quast test_quast_ref - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: f9b9f817bde917c1672a17ad1d072d6c - - path: output/quast/test/aligned_stats/NAx_plot.pdf - - path: output/quast/test/aligned_stats/NGAx_plot.pdf - - path: output/quast/test/aligned_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/NGx_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/gc.icarus.txt - md5sum: bdf3e7481880ee7dafbd53add5291da1 - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/contigs_reports/all_alignments_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.mis_contigs.info - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stderr - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stdout - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.unaligned.info - md5sum: a8505cf206bf53ca369f7e3073fee587 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords - md5sum: dda3fc0addc41ecc0d5183dee6f95886 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords.filtered - md5sum: ec9191d0acb5d5bce56b4842551a8598 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords_tmp - md5sum: e5e26685b36489cbcff906fb07320cde - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.sf - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.unaligned - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.used_snps - md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 - - path: output/quast/test/contigs_reports/misassemblies_frcurve_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_report.tex - md5sum: ec1f7a1d1fb4a1b465057cf897b90b51 - - path: output/quast/test/contigs_reports/misassemblies_report.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test/contigs_reports/misassemblies_report.txt - md5sum: 8b9a6d675a41bab6bf344dde2a20a939 - - path: output/quast/test/contigs_reports/transcriptome.mis_contigs.fa - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tex - md5sum: d778f337899736cc62ed837b739b375c - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tsv - md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3 - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.txt - md5sum: fdb440c653e2f0306286798cacceaadb - - path: output/quast/test/contigs_reports/unaligned_report.tex - md5sum: e8e3bcb86da2cbd8eded980de80fa45c - - path: output/quast/test/contigs_reports/unaligned_report.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/test/contigs_reports/unaligned_report.txt - md5sum: 7e6ba6918574fd4b4cf090ead9a55d78 - - path: output/quast/test/genome_stats/features_cumulative_plot.pdf - - path: output/quast/test/genome_stats/features_frcurve_plot.pdf - - path: output/quast/test/genome_stats/genome_info.txt - md5sum: d0193b322079565dc78608291e9c44d1 - - path: output/quast/test/genome_stats/transcriptome_gaps.txt - md5sum: c52381f09ea40b6141be5232494727b6 - - path: output/quast/test/genome_stats/transcriptome_genomic_features_any.txt - md5sum: 307b3bb1f42fc2f11a60a2e9846021d7 - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/alignment_viewer.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: 881df38fdcd5ce2a7b78ac3cbfebbde1 - - path: output/quast/test/report.tsv - md5sum: f9b9f817bde917c1672a17ad1d072d6c - - path: output/quast/test/report.txt - md5sum: dd24fa9b6f95676006dc0928130d7d0b - - path: output/quast/test/transposed_report.tex - md5sum: 8d74e5b3d7967820b0e61acdeeee6dcb - - path: output/quast/test/transposed_report.tsv - md5sum: c0a0d2f998087b307f1a372ed31f5cde - - path: output/quast/test/transposed_report.txt - md5sum: 1dacbc04dfea073cbd74488d8b3cf821 - - path: output/quast/test_misassemblies.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test_unaligned.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/versions.yml - -- name: quast test_quast_noref_nogff - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_noref_nogff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: e76bb5838fcf3fb5a4841f83a8c33a32 - - path: output/quast/test/report.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/report.txt - md5sum: 2c39a11678f941cc927305019a13f478 - - path: output/quast/test/transposed_report.tex - md5sum: 12b4d146d5f48cf4817eafbfa5b8820f - - path: output/quast/test/transposed_report.tsv - md5sum: 0d6da89a9b434069b7c7b8f09884cc70 - - path: output/quast/test/transposed_report.txt - md5sum: f3c8820d6a3a13c5b891f772b8b4a887 - - path: output/quast/versions.yml - -- name: quast test_quast_nogff - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_nogff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: 665d29c4767bb42355b8a9302bace646 - - path: output/quast/test/aligned_stats/NAx_plot.pdf - - path: output/quast/test/aligned_stats/NGAx_plot.pdf - - path: output/quast/test/aligned_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/NGx_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/gc.icarus.txt - md5sum: bdf3e7481880ee7dafbd53add5291da1 - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/contigs_reports/all_alignments_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.mis_contigs.info - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stderr - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stdout - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.unaligned.info - md5sum: a8505cf206bf53ca369f7e3073fee587 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords - md5sum: dda3fc0addc41ecc0d5183dee6f95886 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords.filtered - md5sum: ec9191d0acb5d5bce56b4842551a8598 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords_tmp - md5sum: e5e26685b36489cbcff906fb07320cde - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.sf - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.unaligned - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.used_snps - md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 - - path: output/quast/test/contigs_reports/misassemblies_frcurve_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_report.tex - md5sum: ec1f7a1d1fb4a1b465057cf897b90b51 - - path: output/quast/test/contigs_reports/misassemblies_report.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test/contigs_reports/misassemblies_report.txt - md5sum: 8b9a6d675a41bab6bf344dde2a20a939 - - path: output/quast/test/contigs_reports/transcriptome.mis_contigs.fa - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tex - md5sum: d778f337899736cc62ed837b739b375c - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tsv - md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3 - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.txt - md5sum: fdb440c653e2f0306286798cacceaadb - - path: output/quast/test/contigs_reports/unaligned_report.tex - md5sum: e8e3bcb86da2cbd8eded980de80fa45c - - path: output/quast/test/contigs_reports/unaligned_report.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/test/contigs_reports/unaligned_report.txt - md5sum: 7e6ba6918574fd4b4cf090ead9a55d78 - - path: output/quast/test/genome_stats/genome_info.txt - md5sum: 8186ae63e910796afff33cf000885b74 - - path: output/quast/test/genome_stats/transcriptome_gaps.txt - md5sum: c52381f09ea40b6141be5232494727b6 - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/alignment_viewer.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: 35243bf9fb51f6a11fac0cfe4556a9a9 - - path: output/quast/test/report.tsv - md5sum: 665d29c4767bb42355b8a9302bace646 - - path: output/quast/test/report.txt - md5sum: d7d2a1a477c74e70f6a906d02c88b36b - - path: output/quast/test/transposed_report.tex - md5sum: 77190dcdd1acb8cb8692c9da523e26f8 - - path: output/quast/test/transposed_report.tsv - md5sum: bc2bddf6a787e835ff9c77dfc1a49458 - - path: output/quast/test/transposed_report.txt - md5sum: 395352dadaf01d490b250d2bffef4dea - - path: output/quast/test_misassemblies.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test_unaligned.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/versions.yml - -- name: quast test_quast_noref - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_noref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: e76bb5838fcf3fb5a4841f83a8c33a32 - - path: output/quast/test/report.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/report.txt - md5sum: 2c39a11678f941cc927305019a13f478 - - path: output/quast/test/transposed_report.tex - md5sum: 12b4d146d5f48cf4817eafbfa5b8820f - - path: output/quast/test/transposed_report.tsv - md5sum: 0d6da89a9b434069b7c7b8f09884cc70 - - path: output/quast/test/transposed_report.txt - md5sum: f3c8820d6a3a13c5b891f772b8b4a887 - - path: output/quast/versions.yml