From d2922342125f522a952d235d4ffe3e3618200980 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 9 Jul 2024 10:06:04 +0200 Subject: [PATCH 01/20] fix stubs and add stub tests --- modules/nf-core/untar/main.nf | 14 +- modules/nf-core/untar/tests/main.nf.test | 47 +++++- modules/nf-core/untar/tests/main.nf.test.snap | 152 +++++++++++++++--- 3 files changed, 188 insertions(+), 25 deletions(-) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8a75bb957d1..7ca3b3efe34 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -53,7 +53,19 @@ process UNTAR { prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ mkdir $prefix - touch ${prefix}/file.txt + ## Ensures --strip-components only applied when top level of tar contents is a directory + ## If just files or multiple directories, place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + for i in `tar -tf ${archive}`; + do + touch \${i} + done + else + for i in `tar -tf ${archive}`; + do + touch ${prefix}/\${i} + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 2a7c97bf81e..f556118ff05 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -3,9 +3,7 @@ nextflow_process { name "Test Process UNTAR" script "../main.nf" process "UNTAR" - tag "modules" - tag "modules_nfcore" - tag "untar" + test("test_untar") { when { @@ -19,10 +17,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar") }, + { assert snapshot(process.out).match() }, ) } - } test("test_untar_onlyfiles") { @@ -38,10 +35,48 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + { assert snapshot(process.out).match() }, ) } + } + + test("test_untar - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } } + test("test_untar_onlyfiles - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 64550292f33..c474d333877 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,42 +1,158 @@ { "test_untar_onlyfiles": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "1": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "versions": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:04:43.984731" + }, + "test_untar_onlyfiles - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + ], + "untar": [ [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] + ], + "versions": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-28T11:49:41.320643" + "timestamp": "2024-07-09T10:05:00.262496" + }, + "test_untar - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:04:52.000213" }, "test_untar": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + ], + "untar": [ [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] ] + ], + "versions": [ + "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-28T11:49:33.795172" + "timestamp": "2024-07-09T10:04:35.16268" } } \ No newline at end of file From 6fec892706c732eb74b0d9216de3ef9586d978a1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 9 Jul 2024 10:18:22 +0200 Subject: [PATCH 02/20] fix linting --- modules/nf-core/untar/tests/main.nf.test | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index f556118ff05..c957517aaa6 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -3,6 +3,9 @@ nextflow_process { name "Test Process UNTAR" script "../main.nf" process "UNTAR" + tag "modules" + tag "modules_nfcore" + tag "untar" test("test_untar") { From 5eacdc3ff6c7f8e41bd23f25ccf28e17f4134599 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 9 Jul 2024 10:45:09 +0200 Subject: [PATCH 03/20] fix some linting --- .../centrifuge/centrifuge/tests/main.nf.test | 10 +- .../centrifuge/tests/main.nf.test.snap | 22 ++-- .../centrifuge/kreport/tests/main.nf.test | 5 +- .../kreport/tests/main.nf.test.snap | 13 +- .../checkv/updatedatabase/tests/main.nf.test | 16 ++- .../updatedatabase/tests/main.nf.test.snap | 22 +++- .../controlfreec/freec/tests/main.nf.test | 8 +- .../freec/tests/main.nf.test.snap | 25 ++-- .../gatk4/genomicsdbimport/tests/main.nf.test | 41 +++--- .../genomicsdbimport/tests/main.nf.test.snap | 92 +++++++++++--- .../kmcp/compute/tests/main.nf.test.snap | 38 +----- .../kmcp/profile/tests/main.nf.test.snap | 22 +--- .../metamaps/classify/tests/main.nf.test.snap | 120 +++--------------- .../mapdirectly/tests/main.nf.test.snap | 72 ++--------- .../mmseqs/createindex/tests/main.nf.test | 1 + .../createindex/tests/main.nf.test.snap | 12 +- .../mmseqs/linclust/tests/main.nf.test | 11 +- .../mmseqs/linclust/tests/main.nf.test.snap | 27 ++-- modules/nf-core/rtgtools/rocplot/meta.yml | 2 +- .../rtgtools/rocplot/tests/main.nf.test | 1 + .../rtgtools/rocplot/tests/main.nf.test.snap | 6 +- .../tests/main.nf.test.snap | 68 ++++------ 22 files changed, 267 insertions(+), 367 deletions(-) diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test index d83b522abd2..f2713608572 100644 --- a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test +++ b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test @@ -42,10 +42,10 @@ nextflow_process { file(process.out.results[0][1]).name, file(process.out.fastq_mapped[0][1][0]).name, file(process.out.fastq_unmapped[0][1][0]).name, + process.out.versions ).match() } ) } - } test("sarscov2_fastq_pe") { @@ -56,8 +56,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = true @@ -73,10 +73,10 @@ nextflow_process { file(process.out.results[0][1]).name, file(process.out.fastq_mapped[0][1][0]).name, file(process.out.fastq_unmapped[0][1][0]).name, + process.out.versions ).match() } ) } - } test("sarscov2_fastq_se_stub") { @@ -100,7 +100,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap index f8a2ef7b8b6..a981e51793f 100644 --- a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap +++ b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap @@ -92,34 +92,40 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-02T07:47:36.886757827" + "timestamp": "2024-07-09T10:36:42.919054" }, "sarscov2_fastq_se": { "content": [ "test.report.txt", "test.results.txt", "", - "" + "", + [ + "versions.yml:md5,1ce028d9f968eca6df31586fe3b77c84" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-02T08:22:31.470316024" + "timestamp": "2024-07-09T10:36:23.087465" }, "sarscov2_fastq_pe": { "content": [ "test.report.txt", "test.results.txt", "test.mapped.fastq.1.gz", - "test.unmapped.fastq.1.gz" + "test.unmapped.fastq.1.gz", + [ + "versions.yml:md5,1ce028d9f968eca6df31586fe3b77c84" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-02T08:22:48.866073154" + "timestamp": "2024-07-09T10:36:33.471335" } } \ No newline at end of file diff --git a/modules/nf-core/centrifuge/kreport/tests/main.nf.test b/modules/nf-core/centrifuge/kreport/tests/main.nf.test index 6347bd7cc50..6d4bc6b1d2a 100644 --- a/modules/nf-core/centrifuge/kreport/tests/main.nf.test +++ b/modules/nf-core/centrifuge/kreport/tests/main.nf.test @@ -50,8 +50,9 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.kreport[0][1]).name, + process.out.versions ).match() } - ) + ) } } @@ -75,7 +76,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap b/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap index 4e0aaa79182..3d638acd8b9 100644 --- a/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap +++ b/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap @@ -30,18 +30,21 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-02T06:18:36.794405448" + "timestamp": "2024-07-09T10:37:05.883784" }, "sarscov2_fastq_se": { "content": [ - "test.txt" + "test.txt", + [ + "versions.yml:md5,43c766a19f2edf7e05d1a2a0b1816b13" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-02T06:28:20.461891873" + "timestamp": "2024-07-09T10:36:53.971559" } } \ No newline at end of file diff --git a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test index 2f59da973fa..5a82c80e539 100644 --- a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test +++ b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test @@ -48,6 +48,8 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() }, + { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() }, { assert snapshot( "${process.out.checkv_db.get(0).get(1).get(0)}", "${process.out.checkv_db.get(0).get(1).get(2)}", @@ -57,11 +59,10 @@ nextflow_process { "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.faa", "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.fna", "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.log", - "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv" + "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv", + process.out.versions ).match() }, - { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() }, - { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() } ) } } @@ -84,6 +85,8 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() }, + { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() }, { assert snapshot( "${process.out.checkv_db.get(0).get(1).get(0)}", "${process.out.checkv_db.get(0).get(1).get(2)}", @@ -93,11 +96,10 @@ nextflow_process { "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.faa", "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.fna", "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.log", - "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv" + "${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv", + process.out.versions ).match() - }, - { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() }, - { assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() } + } ) } } diff --git a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test.snap b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test.snap index e10cfce143e..d0a06a2713c 100644 --- a/modules/nf-core/checkv/updatedatabase/tests/main.nf.test.snap +++ b/modules/nf-core/checkv/updatedatabase/tests/main.nf.test.snap @@ -15,9 +15,16 @@ "checkv_reps.faa:md5,6f1e81fbab2d6f39367e3a037df1eec9", "checkv_reps.fna:md5,5f7b89beb65e7405ff2214c2a7c981ba", "checkv_reps.log:md5,ebd0238f4df0fa5f3a8af40cd2646f84", - "checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c" + "checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c", + [ + "versions.yml:md5,e2bdb90d427b1d7b5d3ff4555230cdcd" + ] ], - "timestamp": "2024-01-17T17:19:49.436344753" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:39:34.796067" }, "sarscov2 - genome - genome_fasta": { "content": [ @@ -35,8 +42,15 @@ "checkv_reps.faa:md5,6f1e81fbab2d6f39367e3a037df1eec9", "checkv_reps.fna:md5,5f7b89beb65e7405ff2214c2a7c981ba", "checkv_reps.log:md5,ebd0238f4df0fa5f3a8af40cd2646f84", - "checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c" + "checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c", + [ + "versions.yml:md5,e2bdb90d427b1d7b5d3ff4555230cdcd" + ] ], - "timestamp": "2023-12-11T15:51:27.123218646" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:39:17.749242" } } \ No newline at end of file diff --git a/modules/nf-core/controlfreec/freec/tests/main.nf.test b/modules/nf-core/controlfreec/freec/tests/main.nf.test index 90312aebc80..8e38becdfdc 100644 --- a/modules/nf-core/controlfreec/freec/tests/main.nf.test +++ b/modules/nf-core/controlfreec/freec/tests/main.nf.test @@ -70,9 +70,9 @@ nextflow_process { path(process.out.BAF.get(0).get(1)).readLines()[0], path(process.out.ratio.get(0).get(1)).readLines()[0], path(process.out.config.get(0).get(1)).readLines()[0], - path(process.out.info.get(0).get(1)).readLines()[0] - ).match() }, - { assert snapshot(process.out.versions).match("version") } + path(process.out.info.get(0).get(1)).readLines()[0], + process.out.versions + ).match() } ) } @@ -159,7 +159,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/controlfreec/freec/tests/main.nf.test.snap b/modules/nf-core/controlfreec/freec/tests/main.nf.test.snap index 39850d02564..eb0c468ae65 100644 --- a/modules/nf-core/controlfreec/freec/tests/main.nf.test.snap +++ b/modules/nf-core/controlfreec/freec/tests/main.nf.test.snap @@ -178,21 +178,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-26T13:42:56.629043" - }, - "version": { - "content": [ - [ - "versions.yml:md5,e704fc0e6d1ac333dc419498fa128769" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-03-27T10:01:40.977048" + "timestamp": "2024-07-09T10:41:07.003311" }, "human - mpileup": { "content": [ @@ -201,12 +189,15 @@ "Chromosome\tPosition\tBAF\tFittedA\tFittedB\tA\tB\tuncertainty", "Chromosome\tStart\tRatio\tMedianRatio\tCopyNumber\tBAF\testimatedBAF\tGenotype\tUncertaintyOfGT", "[general]", - "Program_Version\tv11.6" + "Program_Version\tv11.6", + [ + "versions.yml:md5,e704fc0e6d1ac333dc419498fa128769" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T10:14:50.936823" + "timestamp": "2024-07-09T10:40:42.538035" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test index 9c207b30744..5fef5dd2544 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test @@ -17,11 +17,11 @@ nextflow_process { """ // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , - [] , - [] ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , + [] , + [] ] // run_intlist input[1] = false // run_updatewspace @@ -36,12 +36,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.genomicsdb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(file(process.out.updatedb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(process.out.intervallist.get(0).get(1)).match() } + { assert snapshot( + file(process.out.genomicsdb.get(0).get(1)).list().sort(), + process.out.versions + ).match() } ) } - } test("test_gatk4_genomicsdbimport_get_intervalslist") { @@ -76,10 +78,12 @@ nextflow_process { { assert process.success }, //{ assert snapshot(file(process.out.genomicsdb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(file(process.out.updatedb.get(0).get(1)).list().sort()).match() } - { assert snapshot(process.out.intervallist.get(0).get(1)).match() } + { assert snapshot( + process.out.intervallist.get(0).get(1), + process.out.versions + ).match() } ) } - } test("test_gatk4_genomicsdbimport_update_genomicsdb") { @@ -113,11 +117,13 @@ nextflow_process { assertAll( { assert process.success }, //{ assert snapshot(file(process.out.genomicsdb.get(0).get(1)).list().sort()).match() } - { assert snapshot(file(process.out.updatedb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(process.out.intervallist.get(0).get(1)).match() } + { assert snapshot( + file(process.out.updatedb.get(0).get(1)).list().sort(), + process.out.versions + ).match() } ) } - } test("test_gatk4_genomicsdbimport_stub") { @@ -129,11 +135,11 @@ nextflow_process { """ // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , - [] , - [] ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , + [] , + [] ] // run_intlist input[1] = false // run_updatewspace @@ -147,9 +153,8 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert snapshot(process.out).match()} ) } - } - } diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap index a633bbdc16c..55ced0d8802 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap @@ -1,40 +1,98 @@ { "test_gatk4_genomicsdbimport_get_intervalslist": { "content": [ - "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf" + "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf", + [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-28T17:55:03.846241" + "timestamp": "2024-07-09T10:42:51.836379" }, "test_gatk4_genomicsdbimport_create_genomicsdb": { "content": [ - "__tiledb_workspace.tdb", - "callset.json", - "chr22$1$40001", - "vcfheader.vcf", - "vidmap.json" + [ + "__tiledb_workspace.tdb", + "callset.json", + "chr22$1$40001", + "vcfheader.vcf", + "vidmap.json" + ], + [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-14T11:22:10.11423157" + "timestamp": "2024-07-09T10:42:36.846239" }, "test_gatk4_genomicsdbimport_update_genomicsdb": { "content": [ - "__tiledb_workspace.tdb", - "callset.json", - "chr22$1$40001", - "vcfheader.vcf", - "vidmap.json" + [ + "__tiledb_workspace.tdb", + "callset.json", + "chr22$1$40001", + "vcfheader.vcf", + "vidmap.json" + ], + [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-14T12:46:42.403794676" + "timestamp": "2024-07-09T10:43:09.00769" + }, + "test_gatk4_genomicsdbimport_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ], + "genomicsdb": [ + [ + { + "id": "test" + }, + "test:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "intervallist": [ + + ], + "updatedb": [ + + ], + "versions": [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:43:20.921712" } } \ No newline at end of file diff --git a/modules/nf-core/kmcp/compute/tests/main.nf.test.snap b/modules/nf-core/kmcp/compute/tests/main.nf.test.snap index 486cc73db81..0e7fa976563 100644 --- a/modules/nf-core/kmcp/compute/tests/main.nf.test.snap +++ b/modules/nf-core/kmcp/compute/tests/main.nf.test.snap @@ -3,46 +3,22 @@ "content": [ { "0": [ - [ - { - "id": "test" - }, - [ - "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "1": [ - [ - { - "id": "test" - }, - "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ - "versions.yml:md5,58679034c168431cc97ba2a5f9cb34da" + ], "info": [ - [ - { - "id": "test" - }, - "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "outdir": [ - [ - { - "id": "test" - }, - [ - "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "versions": [ - "versions.yml:md5,58679034c168431cc97ba2a5f9cb34da" + ] } ], @@ -50,7 +26,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-06T15:32:15.886382037" + "timestamp": "2024-07-09T10:22:52.554318" }, "sarscov2 - fasta": { "content": [ diff --git a/modules/nf-core/kmcp/profile/tests/main.nf.test.snap b/modules/nf-core/kmcp/profile/tests/main.nf.test.snap index 72b41ce8d61..d3aab5e5615 100644 --- a/modules/nf-core/kmcp/profile/tests/main.nf.test.snap +++ b/modules/nf-core/kmcp/profile/tests/main.nf.test.snap @@ -3,28 +3,16 @@ "content": [ { "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test_kmcp.profile:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - "versions.yml:md5,71f3499117cd6d006be15365b761d38b" + ], "profile": [ - [ - { - "id": "test", - "single_end": true - }, - "test_kmcp.profile:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,71f3499117cd6d006be15365b761d38b" + ] } ], @@ -32,7 +20,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-07T15:36:20.331533599" + "timestamp": "2024-07-09T10:22:21.367706" }, "sarscov2 - fasta": { "content": [ diff --git a/modules/nf-core/metamaps/classify/tests/main.nf.test.snap b/modules/nf-core/metamaps/classify/tests/main.nf.test.snap index 506ff28627c..ca98d1a1836 100644 --- a/modules/nf-core/metamaps/classify/tests/main.nf.test.snap +++ b/modules/nf-core/metamaps/classify/tests/main.nf.test.snap @@ -146,143 +146,59 @@ "content": [ { "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.WIMP:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.evidenceUnknownSpecies:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.reads2Taxon:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "4": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.contigCoverage:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "5": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.lengthAndIdentitiesPerMappingUnit:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "6": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.reads2Taxon.krona:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "7": [ - "versions.yml:md5,60993f8b87f7a2e25367c7dc96c9b859" + ], "contig_coverage": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.contigCoverage:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "em": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "evidence_unknown_species": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.evidenceUnknownSpecies:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "krona": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.reads2Taxon.krona:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "length_and_id": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.lengthAndIdentitiesPerMappingUnit:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "reads2taxon": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.reads2Taxon:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,60993f8b87f7a2e25367c7dc96c9b859" + ], "wimp": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.EM.WIMP:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T10:56:30.641353" + "timestamp": "2024-07-09T10:26:19.525254" } } \ No newline at end of file diff --git a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap index e552413685e..741e6cd1fe9 100644 --- a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap +++ b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap @@ -3,90 +3,42 @@ "content": [ { "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.meta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.meta.unmappedReadsLengths:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.parameters:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "4": [ - "versions.yml:md5,54af95dffcf4481d255c84d70cf851ef" + ], "classification_res": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "meta_file": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.meta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "meta_unmappedreadsLengths": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.meta.unmappedReadsLengths:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "para_file": [ - [ - { - "id": "test", - "single_end": true - }, - "test_classification_res.parameters:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,54af95dffcf4481d255c84d70cf851ef" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T14:12:30.932597" + "timestamp": "2024-07-09T10:25:56.684566" }, "sarscov2_nanopore_mapdirectly": { "content": [ diff --git a/modules/nf-core/mmseqs/createindex/tests/main.nf.test b/modules/nf-core/mmseqs/createindex/tests/main.nf.test index f47ccc3757d..543c91b0093 100644 --- a/modules/nf-core/mmseqs/createindex/tests/main.nf.test +++ b/modules/nf-core/mmseqs/createindex/tests/main.nf.test @@ -8,6 +8,7 @@ nextflow_process { tag "modules_nfcore" tag "mmseqs" tag "mmseqs/createindex" + tag "untar" test("sars-cov-2 - mmseqs.tar.gz") { diff --git a/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap index b0fde15d69c..cd59a2fea63 100644 --- a/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap @@ -5,7 +5,11 @@ "versions.yml:md5,63073370e7d20afd4773f5e6e7581582" ] ], - "timestamp": "2023-11-28T11:59:51.777561277" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:43:46.152721" }, "createindex_filtered_files": { "content": [ @@ -49,6 +53,10 @@ "mmseqs_seq_h.index:md5,0040e6a02964914a87ef1efbe9011cbf" ] ], - "timestamp": "2023-11-28T11:59:51.728054679" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:43:46.077636" } } \ No newline at end of file diff --git a/modules/nf-core/mmseqs/linclust/tests/main.nf.test b/modules/nf-core/mmseqs/linclust/tests/main.nf.test index 02a6cd6259a..02383ae3409 100644 --- a/modules/nf-core/mmseqs/linclust/tests/main.nf.test +++ b/modules/nf-core/mmseqs/linclust/tests/main.nf.test @@ -8,6 +8,7 @@ nextflow_process { tag "modules_nfcore" tag "mmseqs" tag "mmseqs/linclust" + tag "untar" test("Should cluster an mmseqs database") { @@ -40,12 +41,14 @@ nextflow_process { File[] listOfFiles = folder.listFiles() listOfFiles = listOfFiles.sort { it.name } assert listOfFiles.length == 4 - assert snapshot("${get(0).get(1)}/${listOfFiles[0].name}").match("test_output_cluster.0") - assert snapshot("${get(0).get(1)}/${listOfFiles[2].name}").match("test_output_cluster.dbtype") - assert snapshot("${get(0).get(1)}/${listOfFiles[3].name}").match("test_output_cluster.index") + assert snapshot( + "${get(0).get(1)}/${listOfFiles[0].name}", + "${get(0).get(1)}/${listOfFiles[2].name}", + "${get(0).get(1)}/${listOfFiles[3].name}", + process.out.versions + ).match() } }, - { assert process.out.versions } ) } } diff --git a/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap b/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap index 9922e0e4984..c3c986470ee 100644 --- a/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap @@ -1,20 +1,17 @@ { - "test_output_cluster.index": { + "Should cluster an mmseqs database": { "content": [ - "test_output_cluster.index:md5,38908275cdd5727ae0eb9be017f9ca13" + "test_output_cluster.0:md5,fe0181e97deccd7c807e9c14f81ebdc0", + "test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089", + "test_output_cluster.index:md5,38908275cdd5727ae0eb9be017f9ca13", + [ + "versions.yml:md5,65ce4e8b36259f881d11b0d8caaee69a" + ] ], - "timestamp": "2023-11-21T15:28:32.839871644" - }, - "test_output_cluster.0": { - "content": [ - "test_output_cluster.0:md5,fe0181e97deccd7c807e9c14f81ebdc0" - ], - "timestamp": "2023-11-21T15:28:32.805287285" - }, - "test_output_cluster.dbtype": { - "content": [ - "test_output_cluster.dbtype:md5,5c879eb8a8613fd4537b919e7d68d089" - ], - "timestamp": "2023-11-21T15:28:32.829174852" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:43:54.574245" } } \ No newline at end of file diff --git a/modules/nf-core/rtgtools/rocplot/meta.yml b/modules/nf-core/rtgtools/rocplot/meta.yml index 927cff90c35..2b4d43d7c91 100644 --- a/modules/nf-core/rtgtools/rocplot/meta.yml +++ b/modules/nf-core/rtgtools/rocplot/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index 160eafcf901..9a5fed2620f 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modules_nfcore" tag "rtgtools" tag "rtgtools/rocplot" + tag "untar" test("homo_sapiens - tsv") { diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap index 389ffb5bb15..f4dee3a1b96 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap @@ -5,6 +5,10 @@ "test.svg", "versions.yml" ], - "timestamp": "2023-10-24T12:48:36.35343056" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:44:42.642303" } } \ No newline at end of file diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap index 6989f937e2f..931ae42444d 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap @@ -2,36 +2,26 @@ "gene_log_multi_matrix_rowdata_coldataa_stub": { "content": [ [ - [ - { - "id": "test" - }, - "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-09T13:57:39.545403663" + "timestamp": "2024-07-09T10:16:50.286892" }, "gene_log_single_matrix_stub": { "content": [ [ - [ - { - "id": "test" - }, - "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-09T13:58:23.258210775" + "timestamp": "2024-07-09T10:17:23.425783" }, "versions_single_matrix": { "content": [ @@ -48,19 +38,14 @@ "gene_log_multi_matrix_rowdata_stub": { "content": [ [ - [ - { - "id": "test" - }, - "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-09T13:57:52.234643863" + "timestamp": "2024-07-09T10:17:00.183379" }, "gene_log_multi_matrix_rowdata": { "content": "7c35131fdd46dcdba6c71f7f11d5b2c7", @@ -73,38 +58,38 @@ "versions_multi_matrix_rowdata_stub": { "content": [ [ - "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-08T14:46:04.546156" + "timestamp": "2024-07-09T10:17:00.226729" }, "versions_multi_matrix_stub": { "content": [ [ - "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-08T14:46:21.128541" + "timestamp": "2024-07-09T10:17:11.198137" }, "versions_multi_matrix_rowdata_coldata_stub": { "content": [ [ - "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-08T14:45:43.440258" + "timestamp": "2024-07-09T10:16:50.334806" }, "gene_log_multi_matrix": { "content": "7c35131fdd46dcdba6c71f7f11d5b2c7", @@ -117,19 +102,14 @@ "gene_log_multi_matrix_stub": { "content": [ [ - [ - { - "id": "test" - }, - "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-09T13:58:07.904228634" + "timestamp": "2024-07-09T10:17:11.151926" }, "gene_log_single_matrix": { "content": "7c35131fdd46dcdba6c71f7f11d5b2c7", @@ -142,14 +122,14 @@ "versions_single_matrix_stub": { "content": [ [ - "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-08T14:46:37.670798" + "timestamp": "2024-07-09T10:17:23.466378" }, "versions_multi_matrix_rowdata": { "content": [ From 06d166341e68c12f893c62f323cf5ff5dabb8868 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 9 Jul 2024 10:51:18 +0200 Subject: [PATCH 04/20] fix linting --- modules/nf-core/rtgtools/rocplot/tests/main.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index 9a5fed2620f..0a79a385b94 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modules_nfcore" tag "rtgtools" tag "rtgtools/rocplot" + tag "rtgtools/vcfeval" tag "untar" test("homo_sapiens - tsv") { From 2b570f9d7bfab310dd1a407e33c038dab3b5a875 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 9 Jul 2024 10:56:13 +0200 Subject: [PATCH 05/20] better comment --- modules/nf-core/untar/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 7ca3b3efe34..9ec6bdc4113 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -53,8 +53,7 @@ process UNTAR { prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ mkdir $prefix - ## Ensures --strip-components only applied when top level of tar contents is a directory - ## If just files or multiple directories, place all in prefix + ## Dry-run untaring the archive to get the files and place all in prefix if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then for i in `tar -tf ${archive}`; do From 15697e8c396225357f2f5f4ad5c635f8bfba6342 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 10 Jul 2024 12:06:58 +0200 Subject: [PATCH 06/20] change container --- modules/nf-core/untar/environment.yml | 2 +- modules/nf-core/untar/main.nf | 4 +-- modules/nf-core/untar/tests/main.nf.test.snap | 32 +++++++++---------- 3 files changed, 19 insertions(+), 19 deletions(-) diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb101d0..c2f5f6180e1 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -7,5 +7,5 @@ channels: dependencies: - conda-forge::grep=3.11 - - conda-forge::sed=4.7 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 9ec6bdc4113..af03be10ab8 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index c474d333877..ceb91b7925c 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -13,7 +13,7 @@ ] ], "1": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ], "untar": [ [ @@ -26,15 +26,15 @@ ] ], "versions": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:04:43.984731" + "timestamp": "2024-07-10T12:04:28.231047" }, "test_untar_onlyfiles - stub": { "content": [ @@ -50,7 +50,7 @@ ] ], "1": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ], "untar": [ [ @@ -63,15 +63,15 @@ ] ], "versions": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:05:00.262496" + "timestamp": "2024-07-10T12:04:45.773103" }, "test_untar - stub": { "content": [ @@ -89,7 +89,7 @@ ] ], "1": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ], "untar": [ [ @@ -104,15 +104,15 @@ ] ], "versions": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:04:52.000213" + "timestamp": "2024-07-10T12:04:36.777441" }, "test_untar": { "content": [ @@ -130,7 +130,7 @@ ] ], "1": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ], "untar": [ [ @@ -145,14 +145,14 @@ ] ], "versions": [ - "versions.yml:md5,19efec1f58773173ead5b1253b1ecfa9" + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:04:35.16268" + "timestamp": "2024-07-10T12:04:19.377674" } } \ No newline at end of file From a4edbd1348509e6dfc4ce2853cc86e3ecac29801 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 10 Jul 2024 13:56:18 +0200 Subject: [PATCH 07/20] update snapshots --- .../antismashlite/tests/main.nf.test.snap | 156 +++--------------- .../tests/main.nf.test.snap | 24 +-- .../bracken/build/tests/main.nf.test.snap | 54 +----- .../custom/tx2gene/tests/main.nf.test.snap | 22 +-- .../kmcp/compute/tests/main.nf.test.snap | 40 ++++- .../mmseqs/createtsv/tests/main.nf.test.snap | 26 +-- 6 files changed, 81 insertions(+), 241 deletions(-) diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap index 675829cd715..3a0cf03f9f9 100644 --- a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap +++ b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap @@ -76,67 +76,28 @@ ], "1": [ - [ - { - "id": "test" - }, - [ - [ - "bacteria.css:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "about.svg:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "antismash.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] + ], "10": [ - [ - { - "id": "test" - }, - "genome.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "11": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "12": [ ], "13": [ - [ - { - "id": "test" - }, - "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "14": [ ], "15": [ - [ - { - "id": "test" - }, - "regions.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "16": [ - "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" + ], "2": [ @@ -154,32 +115,13 @@ ], "7": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "8": [ - [ - { - "id": "test" - }, - "genome.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "9": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "clusterblast_file": [ @@ -188,70 +130,22 @@ ], "gbk_input": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "gbk_results": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "html": [ - [ - { - "id": "test" - }, - "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "html_accessory_files": [ - [ - { - "id": "test" - }, - [ - [ - "bacteria.css:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "about.svg:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "antismash.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] + ], "json_results": [ - [ - { - "id": "test" - }, - "genome.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "json_sideloading": [ - [ - { - "id": "test" - }, - "regions.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "knownclusterblast_dir": [ @@ -266,12 +160,7 @@ ], "log": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "svg_files_clusterblast": [ @@ -280,22 +169,17 @@ ], "versions": [ - "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" + ], "zip": [ - [ - { - "id": "test" - }, - "genome.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-09T17:06:15.671842533" + "timestamp": "2024-07-10T12:51:27.443185" } } \ No newline at end of file diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap index 93d071871fa..9699419b8db 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap @@ -3,38 +3,30 @@ "content": [ { "0": [ - [ - - ] + ], "1": [ - [ - - ] + ], "2": [ - "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" + ], "antismash_dir": [ - [ - - ] + ], "database": [ - [ - - ] + ], "versions": [ - "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-07T23:13:12.85814463" + "timestamp": "2024-07-10T12:41:09.808653" }, "antiSMASH-lite downloaddatabases": { "content": [ diff --git a/modules/nf-core/bracken/build/tests/main.nf.test.snap b/modules/nf-core/bracken/build/tests/main.nf.test.snap index 49f4240fee7..e9310926184 100644 --- a/modules/nf-core/bracken/build/tests/main.nf.test.snap +++ b/modules/nf-core/bracken/build/tests/main.nf.test.snap @@ -18,67 +18,29 @@ "content": [ { "0": [ - [ - { - "id": "db" - }, - [ - "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", - "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "1": [ - [ - { - "id": "db" - }, - [ - "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "2": [ - "versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b" + ], "bracken_files": [ - [ - { - "id": "db" - }, - [ - "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "db": [ - [ - { - "id": "db" - }, - [ - "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", - "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", - "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + ], "versions": [ - "versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-04-17T18:41:14.406736156" + "timestamp": "2024-07-10T13:06:03.38959" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index 7bc258353e9..99546243c07 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -36,33 +36,23 @@ "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + ], "tx2gene": [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-05T13:13:24.237507" + "timestamp": "2024-07-10T12:51:45.122072" } } \ No newline at end of file diff --git a/modules/nf-core/kmcp/compute/tests/main.nf.test.snap b/modules/nf-core/kmcp/compute/tests/main.nf.test.snap index 0e7fa976563..a417de49094 100644 --- a/modules/nf-core/kmcp/compute/tests/main.nf.test.snap +++ b/modules/nf-core/kmcp/compute/tests/main.nf.test.snap @@ -3,30 +3,54 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + [ + "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "1": [ - + [ + { + "id": "test" + }, + "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + "versions.yml:md5,58679034c168431cc97ba2a5f9cb34da" ], "info": [ - + [ + { + "id": "test" + }, + "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "outdir": [ - + [ + { + "id": "test" + }, + [ + "_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "versions": [ - + "versions.yml:md5,58679034c168431cc97ba2a5f9cb34da" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:22:52.554318" + "timestamp": "2024-07-10T12:16:52.057965" }, "sarscov2 - fasta": { "content": [ diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap index 5b8f9569d27..ddf92f1fa0e 100644 --- a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap @@ -68,36 +68,24 @@ "content": [ { "0": [ - [ - { - "id": "test_result", - "single_end": true - }, - "test_result.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + ], "tsv": [ - [ - { - "id": "test_result", - "single_end": true - }, - "test_result.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-03-12T11:53:21.386186911" + "timestamp": "2024-07-10T12:57:54.63621" }, "mmseqs/createtsv - bacteroides_fragilis - taxonomy": { "content": [ @@ -134,4 +122,4 @@ }, "timestamp": "2024-03-12T11:52:51.792345007" } -} +} \ No newline at end of file From 796339064540cb95117fd0f49364233272eeb3b9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 10 Jul 2024 14:54:18 +0200 Subject: [PATCH 08/20] improve untar stubs --- modules/nf-core/last/train/main.nf | 2 +- modules/nf-core/last/train/tests/main.nf.test | 3 --- modules/nf-core/last/train/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/untar/main.nf | 7 ++++++- 4 files changed, 11 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 67938716beb..ac921145f76 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -41,7 +41,7 @@ process LAST_TRAIN { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - INDEX_NAME=STUB + INDEX_NAME=\$(basename \$(ls $index/*.des) .des) touch ${prefix}.\$INDEX_NAME.train cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/last/train/tests/main.nf.test b/modules/nf-core/last/train/tests/main.nf.test index 0055f7c05a7..a4168f2a9e9 100644 --- a/modules/nf-core/last/train/tests/main.nf.test +++ b/modules/nf-core/last/train/tests/main.nf.test @@ -44,7 +44,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - genome - contigs - stub") { @@ -82,7 +81,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/last/train/tests/main.nf.test.snap b/modules/nf-core/last/train/tests/main.nf.test.snap index d41a8a63ded..a46b5896e43 100644 --- a/modules/nf-core/last/train/tests/main.nf.test.snap +++ b/modules/nf-core/last/train/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "contigs", "single_end": false }, - "contigs.STUB.train:md5,d41d8cd98f00b204e9800998ecf8427e" + "contigs..des.train:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -20,7 +20,7 @@ "id": "contigs", "single_end": false }, - "contigs.STUB.train:md5,d41d8cd98f00b204e9800998ecf8427e" + "contigs..des.train:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -30,9 +30,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-06-06T23:01:07.091657" + "timestamp": "2024-07-10T14:50:11.528587" }, "sarscov2 - genome - contigs": { "content": [ diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index af03be10ab8..f0603f25b10 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -57,7 +57,12 @@ process UNTAR { if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then for i in `tar -tf ${archive}`; do - touch \${i} + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch \${i} + else + mkdir -p \${i} + fi done else for i in `tar -tf ${archive}`; From 45cc921d1cf75ea49b1de4f2ac3fdff80d0593dd Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 10 Jul 2024 15:08:32 +0200 Subject: [PATCH 09/20] update snapshots --- .../kmcp/profile/tests/main.nf.test.snap | 24 ++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/kmcp/profile/tests/main.nf.test.snap b/modules/nf-core/kmcp/profile/tests/main.nf.test.snap index d3aab5e5615..f4a05eabfa6 100644 --- a/modules/nf-core/kmcp/profile/tests/main.nf.test.snap +++ b/modules/nf-core/kmcp/profile/tests/main.nf.test.snap @@ -3,24 +3,36 @@ "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_kmcp.profile:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + "versions.yml:md5,71f3499117cd6d006be15365b761d38b" ], "profile": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_kmcp.profile:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,71f3499117cd6d006be15365b761d38b" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:22:21.367706" + "timestamp": "2024-07-10T15:07:59.876784" }, "sarscov2 - fasta": { "content": [ From 6e5b70f2cd7404db200ca719d82e9f74babd3663 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 10 Jul 2024 15:15:53 +0200 Subject: [PATCH 10/20] update snapshots --- .../custom/tx2gene/tests/main.nf.test.snap | 20 ++++-- .../mapdirectly/tests/main.nf.test.snap | 72 +++++++++++++++---- 2 files changed, 75 insertions(+), 17 deletions(-) diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index 99546243c07..c19f10f7162 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -36,16 +36,26 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" ], "tx2gene": [ - + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" ] } ], @@ -53,6 +63,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-10T12:51:45.122072" + "timestamp": "2024-07-10T15:15:34.064489" } } \ No newline at end of file diff --git a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap index 741e6cd1fe9..5a04623661e 100644 --- a/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap +++ b/modules/nf-core/metamaps/mapdirectly/tests/main.nf.test.snap @@ -3,42 +3,90 @@ "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.meta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.meta.unmappedReadsLengths:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "3": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.parameters:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "4": [ - + "versions.yml:md5,54af95dffcf4481d255c84d70cf851ef" ], "classification_res": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta_file": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.meta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta_unmappedreadsLengths": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.meta.unmappedReadsLengths:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "para_file": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.parameters:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,54af95dffcf4481d255c84d70cf851ef" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:25:56.684566" + "timestamp": "2024-07-10T15:13:22.720676" }, "sarscov2_nanopore_mapdirectly": { "content": [ From 018166598a93d9e06f8cfd66280c0032e45c1d00 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 10 Jul 2024 17:19:40 +0200 Subject: [PATCH 11/20] update env --- modules/nf-core/custom/tabulartogseagct/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 4 +++- modules/nf-core/gunzip/main.nf | 4 ++-- modules/nf-core/igv/js/environment.yml | 4 +++- modules/nf-core/igv/js/main.nf | 4 ++-- modules/nf-core/shasum/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 2 -- 7 files changed, 12 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/custom/tabulartogseagct/environment.yml b/modules/nf-core/custom/tabulartogseagct/environment.yml index 73cd511d2c6..bb55b68a08e 100644 --- a/modules/nf-core/custom/tabulartogseagct/environment.yml +++ b/modules/nf-core/custom/tabulartogseagct/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=9.1 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 25910b340a5..dfc02a7b54e 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -4,4 +4,6 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 4ae609fb1cf..5e67e3b9bec 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -4,8 +4,8 @@ process GUNZIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) diff --git a/modules/nf-core/igv/js/environment.yml b/modules/nf-core/igv/js/environment.yml index 7604b3c1012..e6046ef8437 100644 --- a/modules/nf-core/igv/js/environment.yml +++ b/modules/nf-core/igv/js/environment.yml @@ -4,4 +4,6 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/igv/js/main.nf b/modules/nf-core/igv/js/main.nf index ba4a1893f7a..a3cf3539aea 100644 --- a/modules/nf-core/igv/js/main.nf +++ b/modules/nf-core/igv/js/main.nf @@ -5,8 +5,8 @@ process IGV_JS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(alignment), path(index) diff --git a/modules/nf-core/shasum/environment.yml b/modules/nf-core/shasum/environment.yml index 1041bc3018b..8af2d378374 100644 --- a/modules/nf-core/shasum/environment.yml +++ b/modules/nf-core/shasum/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=9.1 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index c2f5f6180e1..4f498244afb 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,10 +1,8 @@ name: untar - channels: - conda-forge - bioconda - defaults - dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 From a66b5cd4d54544d3f04a576d893d407222ee86da Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 11 Jul 2024 10:00:20 +0200 Subject: [PATCH 12/20] better --- .../custom/tabulartogseacls/environment.yml | 2 +- modules/nf-core/rgi/main/tests/main.nf.test | 16 ++++++++-------- modules/nf-core/untar/main.nf | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/modules/nf-core/custom/tabulartogseacls/environment.yml b/modules/nf-core/custom/tabulartogseacls/environment.yml index 96c3276dfb6..89ed4246ef0 100644 --- a/modules/nf-core/custom/tabulartogseacls/environment.yml +++ b/modules/nf-core/custom/tabulartogseacls/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=9.1 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/rgi/main/tests/main.nf.test b/modules/nf-core/rgi/main/tests/main.nf.test index fce16564539..1fca563a969 100644 --- a/modules/nf-core/rgi/main/tests/main.nf.test +++ b/modules/nf-core/rgi/main/tests/main.nf.test @@ -16,11 +16,11 @@ nextflow_process { script "modules/nf-core/untar/main.nf" process { """ - file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('data.tar.gz') + file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('card-data.tar.bz2') input[0] = [ [ ], - file("data.tar.gz") + file("card-data.tar.bz2") ] """ } @@ -42,9 +42,9 @@ nextflow_process { when { process { """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) ] input[1] = RGI_CARDANNOTATION.out.db input[2] = [] @@ -74,9 +74,9 @@ nextflow_process { when { process { """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) ] input[1] = RGI_CARDANNOTATION.out.db input[2] = [] diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index f0603f25b10..23f41182519 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -27,7 +27,7 @@ process UNTAR { ## Ensures --strip-components only applied when top level of tar contents is a directory ## If just files or multiple directories, place all in prefix - if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + if [[ \$(tar -tavf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then tar \\ -C $prefix --strip-components 1 \\ -xavf \\ @@ -54,7 +54,7 @@ process UNTAR { """ mkdir $prefix ## Dry-run untaring the archive to get the files and place all in prefix - if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + if [[ \$(tar -tavf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then for i in `tar -tf ${archive}`; do if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; From 1469a028a349596b66ae37a915c7c701d9f459fd Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 11 Jul 2024 12:35:11 +0200 Subject: [PATCH 13/20] use seqera containers --- modules/nf-core/untar/environment.yml | 3 +++ modules/nf-core/untar/main.nf | 17 +++++++++++------ 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 4f498244afb..c8860c28d2f 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -4,6 +4,9 @@ channels: - bioconda - defaults dependencies: + - conda-forge::coreutils=9.5 - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 23f41182519..cbe08c42885 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : - 'nf-core/ubuntu:22.04' }" + 'oras://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:e1e4ff8dd129544f' : + 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:10736d98b4d693d8' }" input: tuple val(meta), path(archive) @@ -27,7 +27,7 @@ process UNTAR { ## Ensures --strip-components only applied when top level of tar contents is a directory ## If just files or multiple directories, place all in prefix - if [[ \$(tar -tavf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + if [[ \$(tar -tavf ${archive} | grep -o -P "/\$" | uniq | wc -l) -eq 1 ]]; then tar \\ -C $prefix --strip-components 1 \\ -xavf \\ @@ -52,9 +52,9 @@ process UNTAR { stub: prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ - mkdir $prefix + mkdir ${prefix} ## Dry-run untaring the archive to get the files and place all in prefix - if [[ \$(tar -tavf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + if [[ \$(tar -tavf ${archive} | grep -o -P "/\$" | uniq | wc -l) -eq 1 ]]; then for i in `tar -tf ${archive}`; do if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; @@ -67,7 +67,12 @@ process UNTAR { else for i in `tar -tf ${archive}`; do - touch ${prefix}/\${i} + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch ${prefix}/\${i} + else + mkdir -p ${prefix}/\${i} + fi done fi From 3610d034b5ad5a7ec9935c17cc96a69a88481293 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 11 Jul 2024 15:44:33 +0200 Subject: [PATCH 14/20] quay.io --- modules/nf-core/untar/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index cbe08c42885..3c945041499 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -5,7 +5,7 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'oras://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:e1e4ff8dd129544f' : - 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:10736d98b4d693d8' }" + 'nf-core/coreutils_grep_gzip_lbzip2_pruned:10736d98b4d693d8' }" input: tuple val(meta), path(archive) From a5f46e7dd1a38726967af49af1705e4e6ca53966 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 11 Jul 2024 15:51:14 +0200 Subject: [PATCH 15/20] proper usage --- modules/nf-core/untar/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 3c945041499..af5730ebee9 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -27,7 +27,7 @@ process UNTAR { ## Ensures --strip-components only applied when top level of tar contents is a directory ## If just files or multiple directories, place all in prefix - if [[ \$(tar -tavf ${archive} | grep -o -P "/\$" | uniq | wc -l) -eq 1 ]]; then + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then tar \\ -C $prefix --strip-components 1 \\ -xavf \\ @@ -54,7 +54,7 @@ process UNTAR { """ mkdir ${prefix} ## Dry-run untaring the archive to get the files and place all in prefix - if [[ \$(tar -tavf ${archive} | grep -o -P "/\$" | uniq | wc -l) -eq 1 ]]; then + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then for i in `tar -tf ${archive}`; do if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; From bb9e0f99eecf9ff2c1e67a13de54134abc5bb1b5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 11 Jul 2024 16:44:19 +0200 Subject: [PATCH 16/20] update snapshots --- .../antismashlite/tests/main.nf.test.snap | 154 +++++++++++++++--- .../metamaps/classify/tests/main.nf.test.snap | 120 ++++++++++++-- .../tests/main.nf.test.snap | 68 +++++--- 3 files changed, 281 insertions(+), 61 deletions(-) diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap index 3a0cf03f9f9..618b06f965a 100644 --- a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap +++ b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap @@ -76,28 +76,67 @@ ], "1": [ - + [ + { + "id": "test" + }, + [ + [ + "bacteria.css:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "about.svg:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "antismash.js:md5,d41d8cd98f00b204e9800998ecf8427e", + "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] ], "10": [ - + [ + { + "id": "test" + }, + "genome.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "11": [ - + [ + { + "id": "test" + }, + [ + "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", + "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "12": [ ], "13": [ - + [ + { + "id": "test" + }, + "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "14": [ ], "15": [ - + [ + { + "id": "test" + }, + "regions.js:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "16": [ - + "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" ], "2": [ @@ -115,13 +154,32 @@ ], "7": [ - + [ + { + "id": "test" + }, + [ + "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", + "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "8": [ - + [ + { + "id": "test" + }, + "genome.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "9": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "clusterblast_file": [ @@ -130,22 +188,70 @@ ], "gbk_input": [ - + [ + { + "id": "test" + }, + [ + "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", + "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "gbk_results": [ - + [ + { + "id": "test" + }, + [ + "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", + "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "html": [ - + [ + { + "id": "test" + }, + "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "html_accessory_files": [ - + [ + { + "id": "test" + }, + [ + [ + "bacteria.css:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "about.svg:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "antismash.js:md5,d41d8cd98f00b204e9800998ecf8427e", + "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] ], "json_results": [ - + [ + { + "id": "test" + }, + "genome.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "json_sideloading": [ - + [ + { + "id": "test" + }, + "regions.js:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "knownclusterblast_dir": [ @@ -160,7 +266,12 @@ ], "log": [ - + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "svg_files_clusterblast": [ @@ -169,10 +280,15 @@ ], "versions": [ - + "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" ], "zip": [ - + [ + { + "id": "test" + }, + "genome.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] } ], @@ -180,6 +296,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-10T12:51:27.443185" + "timestamp": "2024-07-11T16:35:51.079804" } } \ No newline at end of file diff --git a/modules/nf-core/metamaps/classify/tests/main.nf.test.snap b/modules/nf-core/metamaps/classify/tests/main.nf.test.snap index ca98d1a1836..86dd9872748 100644 --- a/modules/nf-core/metamaps/classify/tests/main.nf.test.snap +++ b/modules/nf-core/metamaps/classify/tests/main.nf.test.snap @@ -146,59 +146,143 @@ "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.WIMP:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.evidenceUnknownSpecies:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.reads2Taxon:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "3": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "4": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.contigCoverage:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "5": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.lengthAndIdentitiesPerMappingUnit:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "6": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.reads2Taxon.krona:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "7": [ - + "versions.yml:md5,60993f8b87f7a2e25367c7dc96c9b859" ], "contig_coverage": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.contigCoverage:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "em": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "evidence_unknown_species": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.evidenceUnknownSpecies:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "krona": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.reads2Taxon.krona:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "length_and_id": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.lengthAndIdentitiesPerMappingUnit:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "reads2taxon": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.reads2Taxon:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,60993f8b87f7a2e25367c7dc96c9b859" ], "wimp": [ - + [ + { + "id": "test", + "single_end": true + }, + "test_classification_res.EM.WIMP:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:26:19.525254" + "timestamp": "2024-07-11T16:36:38.639831" } } \ No newline at end of file diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap index 931ae42444d..1460532c773 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test.snap @@ -2,26 +2,36 @@ "gene_log_multi_matrix_rowdata_coldataa_stub": { "content": [ [ - + [ + { + "id": "test" + }, + "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:16:50.286892" + "timestamp": "2024-07-11T16:41:31.796715" }, "gene_log_single_matrix_stub": { "content": [ [ - + [ + { + "id": "test" + }, + "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:17:23.425783" + "timestamp": "2024-07-11T16:42:47.12955" }, "versions_single_matrix": { "content": [ @@ -38,14 +48,19 @@ "gene_log_multi_matrix_rowdata_stub": { "content": [ [ - + [ + { + "id": "test" + }, + "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:17:00.183379" + "timestamp": "2024-07-11T16:41:54.028064" }, "gene_log_multi_matrix_rowdata": { "content": "7c35131fdd46dcdba6c71f7f11d5b2c7", @@ -58,38 +73,38 @@ "versions_multi_matrix_rowdata_stub": { "content": [ [ - + "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:17:00.226729" + "timestamp": "2024-07-11T16:41:54.080728" }, "versions_multi_matrix_stub": { "content": [ [ - + "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:17:11.198137" + "timestamp": "2024-07-11T16:42:21.425746" }, "versions_multi_matrix_rowdata_coldata_stub": { "content": [ [ - + "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:16:50.334806" + "timestamp": "2024-07-11T16:41:31.837174" }, "gene_log_multi_matrix": { "content": "7c35131fdd46dcdba6c71f7f11d5b2c7", @@ -102,14 +117,19 @@ "gene_log_multi_matrix_stub": { "content": [ [ - + [ + { + "id": "test" + }, + "test.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:17:11.151926" + "timestamp": "2024-07-11T16:42:21.370562" }, "gene_log_single_matrix": { "content": "7c35131fdd46dcdba6c71f7f11d5b2c7", @@ -122,14 +142,14 @@ "versions_single_matrix_stub": { "content": [ [ - + "versions.yml:md5,9fb424df9dedf0dc55c95215ae802bb9" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.04.3" }, - "timestamp": "2024-07-09T10:17:23.466378" + "timestamp": "2024-07-11T16:42:47.173221" }, "versions_multi_matrix_rowdata": { "content": [ From 7a2e68d7006db032447bedff9ee37e9c1e9c9c07 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 12 Jul 2024 10:34:49 +0200 Subject: [PATCH 17/20] keep ubuntu for now --- modules/nf-core/untar/environment.yml | 3 --- modules/nf-core/untar/main.nf | 4 ++-- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index c8860c28d2f..4f498244afb 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -4,9 +4,6 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=9.5 - conda-forge::grep=3.11 - - conda-forge::gzip=1.13 - - conda-forge::lbzip2=2.5 - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index af5730ebee9..9bd8f554611 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:e1e4ff8dd129544f' : - 'nf-core/coreutils_grep_gzip_lbzip2_pruned:10736d98b4d693d8' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) From c0790db827ccb6c317304d0ea14522e9823fd6dc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 12 Jul 2024 13:42:11 +0200 Subject: [PATCH 18/20] update tests and snap --- .../tests/main.nf.test | 111 ++++++++++++------ .../tests/main.nf.test.snap | 26 ++-- 2 files changed, 91 insertions(+), 46 deletions(-) diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test index bc7b5a80553..55f5f2f50a1 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test @@ -10,46 +10,47 @@ nextflow_process { tag "antismash/antismashlitedownloaddatabases" tag "untar" - setup { + test("antiSMASH-lite downloaddatabases") { - run("UNTAR", alias: "UNTAR_CSS") { - script "modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [ ], - file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true) - ] - """ + setup { + + run("UNTAR", alias: "UNTAR_CSS") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ ], + file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true) + ] + """ + } } - } - run("UNTAR", alias: "UNTAR_DETECTION") { - script "modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [ ], - file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true) - ] - """ + run("UNTAR", alias: "UNTAR_DETECTION") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ ], + file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true) + ] + """ + } } - } - run("UNTAR", alias: "UNTAR_MODULES") { - script "modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [ ], - file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) - ] - """ + run("UNTAR", alias: "UNTAR_MODULES") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ ], + file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) + ] + """ + } } } - } -test("antiSMASH-lite downloaddatabases") { when { process { """ @@ -64,18 +65,56 @@ test("antiSMASH-lite downloaddatabases") { assertAll( { assert process.success }, { assert snapshot ( - file(process.out.database.get(0)).list().sort(), - process.out.versions, + file(process.out.database.get(0)).list().sort(), + process.out.versions, ).match() } ) } - } test("antiSMASH-lite downloaddatabases - stub") { options "-stub" + setup { + + run("UNTAR", alias: "UNTAR_CSS") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ ], + file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true) + ] + """ + } + } + + run("UNTAR", alias: "UNTAR_DETECTION") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ ], + file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true) + ] + """ + } + } + + run("UNTAR", alias: "UNTAR_MODULES") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ ], + file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true) + ] + """ + } + } + } + when { process { """ @@ -92,7 +131,5 @@ test("antiSMASH-lite downloaddatabases") { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap index 9699419b8db..21ee9d410f5 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap @@ -3,22 +3,30 @@ "content": [ { "0": [ - + [ + + ] ], "1": [ - + [ + + ] ], "2": [ - + "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" ], "antismash_dir": [ - + [ + + ] ], "database": [ - + [ + + ] ], "versions": [ - + "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" ] } ], @@ -26,7 +34,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-10T12:41:09.808653" + "timestamp": "2024-07-12T13:41:29.456143" }, "antiSMASH-lite downloaddatabases": { "content": [ @@ -47,8 +55,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-07T23:12:29.947339678" + "timestamp": "2024-07-12T13:41:08.116244" } } \ No newline at end of file From ceb4a8f56b6083d6022205fd539c077321b184c2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 12 Jul 2024 13:46:18 +0200 Subject: [PATCH 19/20] update test and snapshot --- .../nf-core/bracken/build/tests/main.nf.test | 34 ++++-- .../bracken/build/tests/main.nf.test.snap | 103 ++++++++++++++++-- 2 files changed, 115 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/bracken/build/tests/main.nf.test b/modules/nf-core/bracken/build/tests/main.nf.test index f4168a7eb1c..781c1518436 100644 --- a/modules/nf-core/bracken/build/tests/main.nf.test +++ b/modules/nf-core/bracken/build/tests/main.nf.test @@ -10,18 +10,18 @@ nextflow_process { tag "bracken/build" tag "untar" - setup { - run ("UNTAR") { - script "../../../untar/main.nf" - process { - """ - input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)] - """ + test("kraken2 - db") { + + setup { + run ("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)] + """ + } } } - } - - test("kraken2 - db") { when { process { @@ -41,6 +41,7 @@ nextflow_process { file("${process.out.bracken_files[0][1]}/database100mers.kmer_distrib").name, file("${process.out.bracken_files[0][1]}/database100mers.kraken").name, file("${process.out.bracken_files[0][1]}/database.kraken").name, + process.out.versions ).match() } ) @@ -52,6 +53,17 @@ nextflow_process { options "-stub" + setup { + run ("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)] + """ + } + } + } + when { process { """ @@ -66,7 +78,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/bracken/build/tests/main.nf.test.snap b/modules/nf-core/bracken/build/tests/main.nf.test.snap index e9310926184..910e314aa41 100644 --- a/modules/nf-core/bracken/build/tests/main.nf.test.snap +++ b/modules/nf-core/bracken/build/tests/main.nf.test.snap @@ -6,34 +6,117 @@ "database.kraken", "database100mers.kmer_distrib", "database100mers.kraken", - "database.kraken" + "database.kraken", + [ + "versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-04-17T18:41:03.693430543" + "timestamp": "2024-07-12T13:45:17.37462" }, "kraken2 - db - stub": { "content": [ { "0": [ - + [ + { + "id": "db" + }, + [ + "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + [ + "G46z5ZvKEd.fna:md5,d41d8cd98f00b204e9800998ecf8427e", + "G46z5ZvKEd.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map_MtGz4nUfR3.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map_eNakvrOVZm.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "z_4A5lulyr.fna:md5,d41d8cd98f00b204e9800998ecf8427e", + "z_4A5lulyr.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "1": [ - + [ + { + "id": "db" + }, + [ + "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "2": [ - + "versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b" ], "bracken_files": [ - + [ + { + "id": "db" + }, + [ + "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "db": [ - + [ + { + "id": "db" + }, + [ + "database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e", + "database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e", + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + [ + "G46z5ZvKEd.fna:md5,d41d8cd98f00b204e9800998ecf8427e", + "G46z5ZvKEd.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map_MtGz4nUfR3.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map_eNakvrOVZm.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "z_4A5lulyr.fna:md5,d41d8cd98f00b204e9800998ecf8427e", + "z_4A5lulyr.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e", + "prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ], "versions": [ - + "versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b" ] } ], @@ -41,6 +124,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-10T13:06:03.38959" + "timestamp": "2024-07-12T13:45:26.452181" } } \ No newline at end of file From ef67963eaaa6af0ebffdc082e3f4d67d7010d206 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 12 Jul 2024 13:55:48 +0200 Subject: [PATCH 20/20] update test and snapshot --- .../mmseqs/createtsv/tests/main.nf.test | 3 +- .../mmseqs/createtsv/tests/main.nf.test.snap | 95 +++++++++++-------- 2 files changed, 57 insertions(+), 41 deletions(-) diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test index 99e79e0c8f2..e9d4f9949ca 100644 --- a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test +++ b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test @@ -123,8 +123,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.tsv).match("tsv") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap index ddf92f1fa0e..1087de88d55 100644 --- a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap +++ b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap @@ -1,34 +1,4 @@ { - "versions": { - "content": [ - [ - "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-12T11:53:02.392516336" - }, - "tsv": { - "content": [ - [ - [ - { - "id": "test_result", - "single_end": true - }, - "test_result.tsv:md5,4e7ba50ce2879660dc6595286bf0d097" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-12T11:53:02.311022721" - }, "mmseqs/createtsv - bacteroides_fragilis - taxonomy - stub": { "content": [ { @@ -60,24 +30,36 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-03-12T11:53:11.715695614" + "timestamp": "2024-07-12T13:55:17.642787" }, "mmseqs/createtsv - sarscov2 - cluster - stub": { "content": [ { "0": [ - + [ + { + "id": "test_result", + "single_end": true + }, + "test_result.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" ], "tsv": [ - + [ + { + "id": "test_result", + "single_end": true + }, + "test_result.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ - + "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" ] } ], @@ -85,7 +67,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-10T12:57:54.63621" + "timestamp": "2024-07-12T13:55:33.645454" }, "mmseqs/createtsv - bacteroides_fragilis - taxonomy": { "content": [ @@ -118,8 +100,43 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-12T13:54:45.718678" + }, + "mmseqs/createtsv - sarscov2 - cluster": { + "content": [ + { + "0": [ + [ + { + "id": "test_result", + "single_end": true + }, + "test_result.tsv:md5,4e7ba50ce2879660dc6595286bf0d097" + ] + ], + "1": [ + "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + ], + "tsv": [ + [ + { + "id": "test_result", + "single_end": true + }, + "test_result.tsv:md5,4e7ba50ce2879660dc6595286bf0d097" + ] + ], + "versions": [ + "versions.yml:md5,20a853f50c920d431e5ab7593ca79e6f" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" }, - "timestamp": "2024-03-12T11:52:51.792345007" + "timestamp": "2024-07-12T13:55:02.731974" } } \ No newline at end of file