From 01baaa91a4faef28abf0568108897d5777e41a2e Mon Sep 17 00:00:00 2001 From: YSims Date: Fri, 27 Sep 2024 07:51:38 +0100 Subject: [PATCH] yahs release update (#6695) * update yahs version and output options * update yahs version and output options * add correct datatype in nf-test, new version yahs would attempt scaffolding based on alignment file * add samtools tag --- modules/nf-core/yahs/main.nf | 8 +-- modules/nf-core/yahs/meta.yml | 1 + modules/nf-core/yahs/tests/main.nf.test | 32 +++++++++--- modules/nf-core/yahs/tests/main.nf.test.snap | 52 +++++--------------- 4 files changed, 41 insertions(+), 52 deletions(-) diff --git a/modules/nf-core/yahs/main.nf b/modules/nf-core/yahs/main.nf index 470e5e2c3b58..6475fd91ad87 100644 --- a/modules/nf-core/yahs/main.nf +++ b/modules/nf-core/yahs/main.nf @@ -4,8 +4,8 @@ process YAHS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/yahs:1.2a.2--h7132678_0': - 'biocontainers/yahs:1.2a.2--h7132678_0' }" + 'https://depot.galaxyproject.org/singularity/yahs:1.2--he4a0461_1': + 'biocontainers/yahs:1.2--he4a0461_1' }" input: tuple val(meta), path(hic_map) @@ -13,8 +13,8 @@ process YAHS { path fai output: - tuple val(meta), path("*scaffolds_final.fa") , emit: scaffolds_fasta - tuple val(meta), path("*scaffolds_final.agp"), emit: scaffolds_agp + tuple val(meta), path("*scaffolds_final.fa") , emit: scaffolds_fasta, optional: true + tuple val(meta), path("*scaffolds_final.agp"), emit: scaffolds_agp, optional: true tuple val(meta), path("*bin") , emit: binary path "versions.yml" , emit: versions diff --git a/modules/nf-core/yahs/meta.yml b/modules/nf-core/yahs/meta.yml index bb3112e80387..38869045f392 100644 --- a/modules/nf-core/yahs/meta.yml +++ b/modules/nf-core/yahs/meta.yml @@ -75,3 +75,4 @@ authors: - "@ksenia-krasheninnikova" maintainers: - "@ksenia-krasheninnikova" + - "@yy5" diff --git a/modules/nf-core/yahs/tests/main.nf.test b/modules/nf-core/yahs/tests/main.nf.test index 6e09ff0054b7..ee53a110d92b 100644 --- a/modules/nf-core/yahs/tests/main.nf.test +++ b/modules/nf-core/yahs/tests/main.nf.test @@ -9,18 +9,36 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "yahs" + tag "samtools/view" - test("sarscov2-bed-fasta-fai") { + setup { + run("SAMTOOLS_VIEW") { + script "../../samtools/view" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = [] + """ + } + } + } + + test("homo_sapiens-bam-fasta-fai") { when { process { """ - input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - + input[0] = SAMTOOLS_VIEW.out.bam + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) """ } } diff --git a/modules/nf-core/yahs/tests/main.nf.test.snap b/modules/nf-core/yahs/tests/main.nf.test.snap index a98c16fbec2e..c62caa91904e 100644 --- a/modules/nf-core/yahs/tests/main.nf.test.snap +++ b/modules/nf-core/yahs/tests/main.nf.test.snap @@ -1,67 +1,37 @@ { - "test-yahs": { + "homo_sapiens-bam-fasta-fai": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168" - ] + ], "2": [ - [ - { - "id": "test" - }, - "test.bin:md5,c60503a616a0f7726176febdad3ae186" - ] + ], "3": [ - "versions.yml:md5,007c44dd06fe8686b6f8068314601462" + ], "binary": [ - [ - { - "id": "test" - }, - "test.bin:md5,c60503a616a0f7726176febdad3ae186" - ] + ], "scaffolds_agp": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168" - ] + ], "scaffolds_fasta": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442" - ] + ], "versions": [ - "versions.yml:md5,007c44dd06fe8686b6f8068314601462" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nextflow": "24.04.2" }, - "timestamp": "2024-08-23T08:47:14.869961" + "timestamp": "2024-09-26T22:35:24.103271222" } } \ No newline at end of file