From 8684e27e1061f855822ecc77d5099bc08f858784 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 27 Aug 2024 07:44:04 +1200 Subject: [PATCH] Added nf-test for gstama/polyacleanup (#6299) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../gstama/polyacleanup/tests/main.nf.test | 42 +++++++++++++++++++ .../polyacleanup/tests/main.nf.test.snap | 33 +++++++++++++++ .../gstama/polyacleanup/tests/nextflow.config | 3 ++ tests/config/pytest_modules.yml | 3 -- .../nf-core/gstama/polyacleanup/main.nf | 15 ------- .../gstama/polyacleanup/nextflow.config | 6 --- .../nf-core/gstama/polyacleanup/test.yml | 14 ------- 7 files changed, 78 insertions(+), 38 deletions(-) create mode 100644 modules/nf-core/gstama/polyacleanup/tests/main.nf.test create mode 100644 modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap create mode 100644 modules/nf-core/gstama/polyacleanup/tests/nextflow.config delete mode 100644 tests/modules/nf-core/gstama/polyacleanup/main.nf delete mode 100644 tests/modules/nf-core/gstama/polyacleanup/nextflow.config delete mode 100644 tests/modules/nf-core/gstama/polyacleanup/test.yml diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test new file mode 100644 index 00000000000..c447f001dc0 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test @@ -0,0 +1,42 @@ + +nextflow_process { + + name "Test Process GSTAMA_POLYACLEANUP" + script "../main.nf" + process "GSTAMA_POLYACLEANUP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gstama" + tag "gstama/polyacleanup" + + test("test-gstama-polyacleanup") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.report[0][1]).linesGzip[0..2], + path(process.out.fasta[0][1]).linesGzip[3..7], + path(process.out.tails[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap new file mode 100644 index 00000000000..a9cc2aefef1 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "test-gstama-polyacleanup": { + "content": [ + [ + "polya_num\tpolya_num_count", + "0\t11", + "1\t1" + ], + [ + "GGAAGCACTTTTTTCCTGTATAGCAAAATGAGTTCAAGATATTCTTTGCCTAATTTCAGCTCTAGCTAGAACCAGTCAATATGGAAATAAACAATGAGGGTATCTAACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCCTACCCGAGTTCTCTTGGCTAAATGTGATACGCATTTAAGGCCCAGAACCTGCTGTTTAAAAGGTTGTGGTAAACTATTTTGTATACCAAAGACTTCTCTGTAATAAAGTATGTAAGTACACATGAACATTTTATATGCACGCACATTTTAAATCATCTGCACATTGAGATTCTACACTTTTCTCAAGGGCACATCTCTATTCCGTTTCTTTGTAAATTTGACTTCTACCTAACAATATGCAATTGCTGGGATTTTTTTCCCTAACAGTATGAAAGTTGTCTTTAAATAGTAAAAGCACCACAATCTATTAACACCACATGTTATCTTTAAACTGAAATATTTTAGTGATGTCTTGGACATCAAAATAATTTCTTAAGGTGGACTCTTGAGTATGTGGGTCCAGCCCAGGTCTGCAGTTTGTGCAGACATAGAAAAAAGAGGAACTTTAAATATTCAGAAAAAGTTAACAGGCTAGCTTTAAAATACTGCTGGAAATTAAATTTCTTCAGAGTTGGCAAGCATGGGCTATTGATCAAAATATGAATTAAACGGATTTACATCATTAAGAAAAAAACAAATCCATGTTATTGTGCTGTGAAATTTCCATGATGCCTTTCAAATAGGCTGCTCACAAATTTTTTTATAATTCTAAATCACTCGCTTTTTGATGGAAAAAAGAATACAGATGGACTGTGTTTTACCTATGTGAAAGTCACCAATCCATTTAAAATAAAATCCAAGAGGGCATATACAGTCTAATCAAGTCATCATTTTCCTGATTAATAAGAACTACACTTTACACAAAATACTTTATCAGCAGCTGTTTTCATCAAAAAATCAGTAGTCAGTTTCACAGTTGAAAAAGTTACACATTAAAATATTTTACAATTCATTATATATTCACCAGGTTCCCATTTTCTAAGGGGCTTTTAATATAAAGCAGAATAGAACACTGTCTCTACTAAAAATACAAAAATTAGCTGGGAGTGGTGGCATGCTCCTATAGTCCTAGCTACTCAGGAGGCTGAGGTGGGAGGATGGCTTGAACCCAGGAGGTCAAGGCTGCAGTGAGCCGAAATTGCACCACTGCATTCCAGGCCGGGCAAAAGAGCCAGACCCTGTCTCAAAAAAAAAAGTTTACATTGTATTTCCTACTCTTAGTTACACTAAGCTAGACAGCAGATGACTAGAGGGTGTGATATATTTACTGAGTGACTCGAAATCCATTTTAAACTTGGAAATGTAAAAACTAACTTCTTTCCACTCATTTTCAGGGTCATTACTGAGAGATAATAAATGACAGAATAAGGAAATAATCACTGTAAATACTTAGGGACCTGAATAAGAGAAAGGAAGGGAAAGTAAAGGGATCTAACATTTATTGGGCACCTTCTGTGTTCCAAGGATTGTGATAGGTTCTTTGCATATCTCATGTAATTTAATTCTCACAATGGCCTTACGAAGCAGGTATTATTCCCATTTTACAGACAAAGAAAATGAGTCTTGAGAGCCTGCATAACGTGTCTAACACTACACAGATGAGAGGCAGTGGAACTTGGTTCCAAATCCTAATCTGCTTGATTCCAAGGACCATGATCTGTATATACACTGGGCTTCTAAACAACTCTGCCCCACTGCAGTGAAAAGAGTCTCAAACACAGACTAGAGTCACACAACTTTTGTGTTTCATCCTTCTTCTCCTGTTTGACAATGTCAGTTAAGTTAATGAGCTTTTCCATTGCCTCGACTTGCCTATTCAGGTGCTTCAAATACATCCCACATGCACGACAATAGGACTCCAAAAGCAGGCCAAACCTCTGGCTAAGTGTTTTATTGTGCATCTCAGATCTAAAAGAATCATGCAAAATTAGAAAAATATATATATAGTCTTAAATCAGTATACAAATAATCTTTGCTAAACAATTTAAACACTCATTTTTGAAATCCAATAAATGTTACAATCATACTAATAATAACATTATTCAAAACCTGTAATTTAGAAGCAAAACCACCATGAGTTTCAGGTAGTTCCTGAATATGTGATTAAATAAACATCTAGTTTTTAGGTTTATTTCAACTAGTTTTCATTGACTAATCTCAGTACAAGATATAAAAGCATGAAAAAAGGAAATTGAGCACAAAAATAATCAAATGAAGAGGGAGGGAACAAAGCGCTCAGTGAATGCTGTTTGACTCTTCTGACACACGTCTACGCTTCTTGTTTTCAACTTAACTTCTGGGTTCCATTTTTAAATTTTAACACTTAAAATATCATATTAGATATAAATCTGTTTCTAAATTTATGAAAAGTTATATGGTTTATGACCTGTAACTTTTGAGTACTGCATATATCACATTCTACAAAACATTTTTTATTCTTAATTAGCTTGTTTTTCAGTAAGAACCACGGGAGTTTGACATTATTGTTCTGAATCTCAAGGTAAAACATTTTTTTTCTTTTTTTGGGGATATTTTAATCCATACACACAGTGAAACCTACAGCAATATTCATCTGGACCTAGAAAATTTTACTTAAGTAGAACAAAAATCTTTAAAAATATTTAAGCTCTCATTCATGACTGAAATTTAGTTTTGAATTTATTACTTTTTAAATTTCAAAGAGCAAAAGTTGAGAAGCTCATCACTGGTACAAAATAGTTTTAGTATGGAAAACTCTTCCAGCCAAACATAAACAAAAGTATATAAGTAATACATATTTATAAATCTATTAAGAAAGCAAGTAATATGTACCTTAAGAATTTAATGGGAAAATAATTAGACTTACTTTAAATGCCAAAAGAAAAAGTGCCCAATCCTTTGATTAGTCAATGCTTTCTTCAGTAAAAATCTCACAAGCAAGTTATCCAAATATTGTTCATATTTTAGGACCTAGGTGATTCAAAAAAAACAAATCAGGTTCAGTTTCTGCATGGCCGATCTAAAGAAAATTTTTTCAGAAAGAAAGTGGATATTACTG", + ">ENST00000472972", + "AACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCC", + ">ENST00000359963 CDS=261-1934", + "TTTCTTTAAATAAAAACATGAAGGAACATAAAATTTCTTTTCATGCGCTTAGTTCCTTTCCAGTTCTCGACTTTTTTTGTTTTTTTTTTTTGAGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGTGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTTTCCTGCCTCAGCCTCCTGAATAGCTGGGACTACAGGTGCGCGCCACCACGCCCAGCTATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATATTGACCAGGCTGGTCTCGAACTCCTGACCTCATGATCCTCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGAGAGCCACTGTGCCCAGCCAGTTCTTGACCTTTTCATTTTGTGTTTCTATCAGATGCTCTTCCTTTCCTATGATAAGAGCAGGATTCAATTCTATTAAGATTTTTAAACTGAGTACCTATGTGGGCTTTGGGCGTGCAAAACACAGTGCAGCAATCTCTTCCCAACTATTTGAGCATTCCCTGCATGATATTCTGACATATATGGACTTATGTCTAGATGTCACTTTAGGAGTCTGAAAACATCAGTTGCAGCTTACAAGAGTGGTCAGTCCTTCCTGTTGTGGTTATTTGAAAAAAAAGAAGGGACTATCATCTTAAAGCACAGAGAGAGAGAGAGAGCAGGAGAAAGAGCTGCTGTGGTGGCAGGCAGAAATGTAACTTAAAAAGAAAAAAATCCTTGCCTGGCAAAGTGGCTCATGCCTATAATTCCTGCACTTTGGGAGGCTGAGACAGGAAGATCGCTTGAGTCCAGGAGTTCAAGACTAGCCTGGACAACATAGTGAGACCCTATCTCTACAAAAATAAAAATTAAAAAAAATTAGCCAGGCATGGGCCGGGCATGGTGGCTCAAGCCTTTAATCCCAGCACTTTGGGAGCCCAAGGTGGGTGGATCAGCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACGTGGAGAAACCCCATCTCTACTAAAAATACAAAACAGTAGCCGGATGTGATGGCACATGCCTGTAATCCCAGCTATTTGAGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCAGAGGTTGTGGTGAGCTGAGATGACACTATTGTACCCCAGCCTGGGCAACAAGAGCAAAACTCTGCCTCAAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGATGCATACCTGTAGTCCCAGCTACTCAGGAGGCTGAGTGGGGGGATCACTTAAGCCCAGGAGATCGAGGTTGCAGTGAGCTGTGATTGTGCCACTGCACTCCAGCCTAAGAGACAGAGCAAGACCCTGTCTCAACAAAACAAAACAAAACCAGCAAACATCCTTGGCATAGATAACAGAAGATAAGAACACATACTTTAGGACTATACTAAGGTTGCTGTGTAGGTGAGGAGAAAGCTGAGGGTAGGGGGAAGGGCTAGGATTGGACAACCTTGGGCATTAAAGAAGGGGTTTGAGCAGAGCTGAGTGGGTTTGGCACCTAATACGCAAAGCTTTTTCCACTTTTTTAACTTCCAAGTTACTCTAGGAAAAATCAGAACCTATGGGACAGAATCTAGGAGATGAGAAGGTACAATCTTTTAGAATCATAAAAATAAAAAAGCTTTAGGCATATGCAGAGAGAATGAGACTCAAGAAACCATTGTCTTATAGCACGCATATTAGCCGCAACACAGCAAAACAAAATTTTATTTATTTATTTATTTATTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCATAGTGACTGGTGTGGCCCAGGCACCAGTGCAGCAGTGCAGTCTCAGCTCACTGCAACCTCTGCCTCCTGGGCTCAAATGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTCCACCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTCAGGGTGGTCTCAAACTTTGGACCTCAGGTGATCCACCTGCCTCGGCCTCCCCAAATGCTGAGATTACAG" + ], + [ + "", + ">tail_ENST00000472972", + "", + ">tail_ENST00000359963 CDS=261-1934", + "" + ], + [ + "versions.yml:md5,dff6214a93a250748705dbd8ec455fec" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:44:18.309783" + } +} \ No newline at end of file diff --git a/modules/nf-core/gstama/polyacleanup/tests/nextflow.config b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config new file mode 100644 index 00000000000..0ffcbb55a35 --- /dev/null +++ b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.prefix = { "${meta.id}_tama" } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 4701d847b89..2173ad70cb5 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -524,9 +524,6 @@ gsea/gsea: gstama/collapse: - modules/nf-core/gstama/collapse/** - tests/modules/nf-core/gstama/collapse/** -gstama/polyacleanup: - - modules/nf-core/gstama/polyacleanup/** - - tests/modules/nf-core/gstama/polyacleanup/** gubbins: - modules/nf-core/gubbins/** - tests/modules/nf-core/gubbins/** diff --git a/tests/modules/nf-core/gstama/polyacleanup/main.nf b/tests/modules/nf-core/gstama/polyacleanup/main.nf deleted file mode 100644 index e1ed59663f9..00000000000 --- a/tests/modules/nf-core/gstama/polyacleanup/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GSTAMA_POLYACLEANUP } from '../../../../../modules/nf-core/gstama/polyacleanup/main.nf' - -workflow test_gstama_polyacleanup { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true) - ] - - GSTAMA_POLYACLEANUP ( input ) -} diff --git a/tests/modules/nf-core/gstama/polyacleanup/nextflow.config b/tests/modules/nf-core/gstama/polyacleanup/nextflow.config deleted file mode 100644 index ff4077028bf..00000000000 --- a/tests/modules/nf-core/gstama/polyacleanup/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.prefix = { "${meta.id}_tama" } - -} diff --git a/tests/modules/nf-core/gstama/polyacleanup/test.yml b/tests/modules/nf-core/gstama/polyacleanup/test.yml deleted file mode 100644 index 6a1ed064c0e..00000000000 --- a/tests/modules/nf-core/gstama/polyacleanup/test.yml +++ /dev/null @@ -1,14 +0,0 @@ -- name: gstama polyacleanup test_gstama_polyacleanup - command: nextflow run ./tests/modules/nf-core/gstama/polyacleanup -entry test_gstama_polyacleanup -c ./tests/config/nextflow.config - tags: - - gstama - - gstama/polyacleanup - files: - - path: output/gstama/test_tama.fa.gz - md5sum: 9c768387478e5f966a42c369c0270b09 - - path: output/gstama/test_tama_polya_flnc_report.txt.gz - md5sum: fe3606979ed11538aacd83159f4cff03 - - path: output/gstama/test_tama_tails.fa.gz - md5sum: ba21256c0afe0bda71b3ee66b4c761bf - - path: output/gstama/versions.yml - md5sum: 07ebb812ae13a350d955fab7600b2542