From aba93ac1a7bb2ac6dfeb028ef590f5392bb3fffc Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Fri, 19 Jul 2024 11:33:41 +0000 Subject: [PATCH 1/2] Update tabix and add threads --- modules/nf-core/tabix/bgzip/environment.yml | 2 +- modules/nf-core/tabix/bgzip/main.nf | 4 +- .../tabix/bgzip/tests/main.nf.test.snap | 56 +++++++++--- .../nf-core/tabix/bgziptabix/environment.yml | 2 +- modules/nf-core/tabix/bgziptabix/main.nf | 6 +- .../tabix/bgziptabix/tests/main.nf.test.snap | 50 ++++++++--- modules/nf-core/tabix/tabix/environment.yml | 2 +- modules/nf-core/tabix/tabix/main.nf | 9 +- .../tabix/tabix/tests/main.nf.test.snap | 86 ++++++++++++++----- 9 files changed, 158 insertions(+), 59 deletions(-) diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 361c078b08a..56cc0fb1e5a 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 3065dab0464..67991c74b40 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : - 'biocontainers/htslib:1.19.1--h81da01d_1' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap index 53d59932853..0748143f04d 100644 --- a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap @@ -3,6 +3,10 @@ "content": [ "gzi_compress_test.vcf.gz.gzi" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:52:29.328146" }, "homo_genome_bedgz_compress": { @@ -20,7 +24,7 @@ ], "2": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ], "gzi": [ @@ -34,16 +38,24 @@ ] ], "versions": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ] } ], - "timestamp": "2024-02-19T14:52:12.422209" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:34.159992362" }, "test_stub": { "content": [ "test_stub.vcf.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:52:20.811489" }, "sarscov2_vcf_bgzip_compress": { @@ -61,7 +73,7 @@ ], "2": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ], "gzi": [ @@ -75,11 +87,15 @@ ] ], "versions": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ] } ], - "timestamp": "2024-02-19T14:52:03.706028" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:22.087769106" }, "sarscov2_vcf_bgzip_compress_gzi": { "content": [ @@ -101,7 +117,7 @@ ] ], "2": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ], "gzi": [ [ @@ -120,22 +136,34 @@ ] ], "versions": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ] } ], - "timestamp": "2024-02-19T14:52:29.271494" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:57.15091665" }, "bgzip_test": { "content": [ "bgzip_test.vcf.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:52:03.768295" }, "bedgz_test": { "content": [ "bedgz_test.bed" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:52:12.453855" }, "sarscov2_vcf_bgzip_compress_stub": { @@ -158,7 +186,7 @@ ] ], "2": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ], "gzi": [ [ @@ -177,10 +205,14 @@ ] ], "versions": [ - "versions.yml:md5,e023292de6ee109a44fc67475d658174" + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" ] } ], - "timestamp": "2024-02-19T14:52:20.769619" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:45.219404786" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index c4235872e34..b9644de9d70 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index bcdcf2a689c..05041f49532 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : - 'biocontainers/htslib:1.19.1--h81da01d_1' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -24,7 +24,7 @@ process TABIX_BGZIPTABIX { def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz - tabix $args2 ${prefix}.${input.getExtension()}.gz + tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap index fcecb2e4925..c166ea7288f 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "id": "tbi_test" }, "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4" + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" ] ], "1": [ ], "2": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ], "gz_csi": [ @@ -26,15 +26,19 @@ "id": "tbi_test" }, "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4" + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" ] ], "versions": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ] } ], - "timestamp": "2024-02-19T14:50:51.513838" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:16.053817543" }, "sarscov2_bed_csi": { "content": [ @@ -48,11 +52,11 @@ "id": "csi_test" }, "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43" + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" ] ], "2": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ], "gz_csi": [ [ @@ -60,35 +64,51 @@ "id": "csi_test" }, "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43" + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" ] ], "gz_tbi": [ ], "versions": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ] } ], - "timestamp": "2024-02-19T14:51:00.513777" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:27.667745444" }, "csi_test": { "content": [ "csi_test.bed.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:51:00.548801" }, "csi_stub": { "content": [ "test.bed.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:51:09.218454" }, "tbi_test": { "content": [ "tbi_test.bed.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:50:51.579654" }, "sarscov2_bed_csi_stub": { @@ -113,7 +133,7 @@ ] ], "2": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ], "gz_csi": [ [ @@ -134,10 +154,14 @@ ] ], "versions": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ] } ], - "timestamp": "2024-02-19T14:51:09.164254" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:45.105209991" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 76b45e16c89..cb74c549010 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 1737141d7fb..532b558eff5 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,8 +4,8 @@ process TABIX_TABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : - 'biocontainers/htslib:1.19.1--h81da01d_1' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(tab) @@ -21,7 +21,10 @@ process TABIX_TABIX { script: def args = task.ext.args ?: '' """ - tabix $args $tab + tabix \\ + --threads $task.cpus \\ + $args \\ + $tab cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap index 034e38b688d..77b3bb056a9 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -3,12 +3,20 @@ "content": [ "test.vcf.gz.csi" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-03-04T14:51:59.788002" }, "tbi_gff": { "content": [ "genome.gff3.gz.tbi" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:53:37.420216" }, "sarscov2_gff_tbi": { @@ -19,14 +27,14 @@ { "id": "tbi_gff" }, - "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178" + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" ] ], "1": [ ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ @@ -36,15 +44,19 @@ { "id": "tbi_gff" }, - "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178" + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" ] ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] } ], - "timestamp": "2024-02-19T14:53:37.388157" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:30:08.097194659" }, "sarscov2_bedgz_tbi": { "content": [ @@ -54,14 +66,14 @@ { "id": "tbi_bed" }, - "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8" + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" ] ], "1": [ ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ @@ -71,26 +83,38 @@ { "id": "tbi_bed" }, - "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8" + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" ] ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] } ], - "timestamp": "2024-02-19T14:53:28.879408" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:56.691350166" }, "tbi_vcf": { "content": [ "test.vcf.gz.tbi" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:53:46.402522" }, "vcf_csi": { "content": [ "test.vcf.gz.csi" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:53:54.921189" }, "sarscov2_vcf_tbi": { @@ -101,14 +125,14 @@ { "id": "tbi_vcf" }, - "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf" + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" ] ], "1": [ ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ @@ -118,15 +142,19 @@ { "id": "tbi_vcf" }, - "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf" + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" ] ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] } ], - "timestamp": "2024-02-19T14:53:46.370358" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:30:19.881620622" }, "sarscov2_vcf_csi_stub": { "content": [ @@ -148,7 +176,7 @@ ] ], "2": [ - "versions.yml:md5,3d45df6d80883bad358631069a2940fd" + "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b" ], "csi": [ [ @@ -167,11 +195,15 @@ ] ], "versions": [ - "versions.yml:md5,3d45df6d80883bad358631069a2940fd" + "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b" ] } ], - "timestamp": "2024-03-04T14:51:59.766184" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:30:42.00245281" }, "sarscov2_vcf_csi": { "content": [ @@ -184,34 +216,42 @@ { "id": "vcf_csi" }, - "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03" + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" ] ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ [ { "id": "vcf_csi" }, - "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03" + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" ] ], "tbi": [ ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] } ], - "timestamp": "2024-02-19T14:53:54.886876" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:30:31.015047391" }, "tbi_bed": { "content": [ "test.bed.gz.tbi" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:53:28.947628" } } \ No newline at end of file From cd5632c9b24508e79fe6573bfbbc3fa220ceb69e Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Fri, 19 Jul 2024 12:26:51 +0000 Subject: [PATCH 2/2] fix linting --- modules/nf-core/tabix/tabix/environment.yml | 4 +- modules/nf-core/tabix/tabix/main.nf | 2 +- .../nf-core/tabix/tabix/tests/main.nf.test | 34 ++++---- .../tabix/tabix/tests/main.nf.test.snap | 79 ++++--------------- 4 files changed, 35 insertions(+), 84 deletions(-) diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index cb74c549010..4d1f9dd43ff 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,8 +1,10 @@ name: tabix_tabix + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 532b558eff5..13acd670ea9 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -36,8 +36,8 @@ process TABIX_TABIX { """ touch ${tab}.tbi touch ${tab}.csi - cat <<-END_VERSIONS > versions.yml + cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test index 3a150c708fb..38fbdfdd34f 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -25,11 +25,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_bed") - } + process.out, + file(process.out.tbi[0][1]).name + ).match() } ) } } @@ -50,11 +49,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_gff") - } + process.out, + file(process.out.tbi[0][1]).name).match() } ) } @@ -76,11 +73,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_vcf") - } + process.out, + file(process.out.tbi[0][1]).name + ).match() } ) } @@ -102,11 +98,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.csi[0][1]).name - ).match("vcf_csi") - } + process.out, + file(process.out.csi[0][1]).name + ).match() } ) } @@ -129,11 +124,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.csi[0][1]).name - ).match("vcf_csi_stub") - } + process.out, + file(process.out.csi[0][1]).name + ).match() } ) } diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap index 77b3bb056a9..c2b9ed0b800 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -1,24 +1,4 @@ { - "vcf_csi_stub": { - "content": [ - "test.vcf.gz.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-03-04T14:51:59.788002" - }, - "tbi_gff": { - "content": [ - "genome.gff3.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-02-19T14:53:37.420216" - }, "sarscov2_gff_tbi": { "content": [ { @@ -50,13 +30,14 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "genome.gff3.gz.tbi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-19T11:30:08.097194659" + "timestamp": "2024-07-19T12:06:25.653807564" }, "sarscov2_bedgz_tbi": { "content": [ @@ -89,33 +70,14 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-19T11:29:56.691350166" - }, - "tbi_vcf": { - "content": [ - "test.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-02-19T14:53:46.402522" - }, - "vcf_csi": { - "content": [ - "test.vcf.gz.csi" + }, + "test.bed.gz.tbi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-02-19T14:53:54.921189" + "timestamp": "2024-07-19T12:06:09.754082161" }, "sarscov2_vcf_tbi": { "content": [ @@ -148,13 +110,14 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "test.vcf.gz.tbi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-19T11:30:19.881620622" + "timestamp": "2024-07-19T12:06:40.042648294" }, "sarscov2_vcf_csi_stub": { "content": [ @@ -176,7 +139,7 @@ ] ], "2": [ - "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ [ @@ -195,15 +158,16 @@ ] ], "versions": [ - "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "test.vcf.gz.csi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-19T11:30:42.00245281" + "timestamp": "2024-07-19T12:07:08.700367261" }, "sarscov2_vcf_csi": { "content": [ @@ -236,22 +200,13 @@ "versions": [ "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-19T11:30:31.015047391" - }, - "tbi_bed": { - "content": [ - "test.bed.gz.tbi" + }, + "test.vcf.gz.csi" ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-02-19T14:53:28.947628" + "timestamp": "2024-07-19T12:06:55.362067748" } } \ No newline at end of file