From 39530b5ca710e028fdec94a704e5eed3f78c5800 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 29 Apr 2022 21:05:12 +0200 Subject: [PATCH] Bump DIAMOND version to 2.0.15 --- modules/diamond/blastp/main.nf | 8 +++----- modules/diamond/blastx/main.nf | 8 +++----- modules/diamond/makedb/main.nf | 8 +++----- tests/config/test_data.config | 1 + tests/modules/diamond/blastp/main.nf | 8 ++++---- tests/modules/diamond/blastp/test.yml | 8 ++++---- tests/modules/diamond/blastx/main.nf | 4 ++-- tests/modules/diamond/blastx/test.yml | 3 ++- tests/modules/diamond/makedb/main.nf | 2 +- tests/modules/diamond/makedb/test.yml | 9 +++++---- 10 files changed, 28 insertions(+), 31 deletions(-) diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf index d7c53d6f..ccd455f4 100644 --- a/modules/diamond/blastp/main.nf +++ b/modules/diamond/blastp/main.nf @@ -2,12 +2,10 @@ process DIAMOND_BLASTP { tag "$meta.id" label 'process_medium' - // Dimaond is limited to v2.0.9 because there is not a - // singularity version higher than this at the current time. - conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null) + conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : - 'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" + 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : + 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf index 6703c1e4..357427eb 100644 --- a/modules/diamond/blastx/main.nf +++ b/modules/diamond/blastx/main.nf @@ -2,12 +2,10 @@ process DIAMOND_BLASTX { tag "$meta.id" label 'process_medium' - // Dimaond is limited to v2.0.9 because there is not a - // singularity version higher than this at the current time. - conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null) + conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : - 'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" + 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : + 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/diamond/makedb/main.nf b/modules/diamond/makedb/main.nf index e3d62f00..a76a94e5 100644 --- a/modules/diamond/makedb/main.nf +++ b/modules/diamond/makedb/main.nf @@ -2,12 +2,10 @@ process DIAMOND_MAKEDB { tag "$fasta" label 'process_medium' - // Dimaond is limited to v2.0.9 because there is not a - // singularity version higher than this at the current time. - conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null) + conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : - 'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" + 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' : + 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }" input: path fasta diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 5d5535c4..62e38c4d 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -14,6 +14,7 @@ params { genome_paf = "${test_data_dir}/genomics/sarscov2/genome/genome.paf" genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes" transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta" + proteome_fasta = "${test_data_dir}/genomics/sarscov2/genome/proteome.fasta" transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf" test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed" diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf index 5c1459d8..80ea2ec5 100644 --- a/tests/modules/diamond/blastp/main.nf +++ b/tests/modules/diamond/blastp/main.nf @@ -7,8 +7,8 @@ include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf' workflow test_diamond_blastp { - db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] + db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] + fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] outext = 'txt' DIAMOND_MAKEDB ( db ) @@ -17,8 +17,8 @@ workflow test_diamond_blastp { workflow test_diamond_blastp_daa { - db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] + db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] + fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] outext = 'daa' DIAMOND_MAKEDB ( db ) diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml index cb297743..c2b8b6f5 100644 --- a/tests/modules/diamond/blastp/test.yml +++ b/tests/modules/diamond/blastp/test.yml @@ -1,19 +1,19 @@ - name: diamond blastp test_diamond_blastp command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config tags: - - diamond - diamond/blastp + - diamond files: - path: output/diamond/test.diamond_blastp.txt - md5sum: 3ca7f6290c1d8741c573370e6f8b4db0 + md5sum: 2515cf88590afa32356497e79a51fce9 - path: output/diamond/versions.yml - name: diamond blastp test_diamond_blastp_daa command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config tags: - - diamond - diamond/blastp + - diamond files: - path: output/diamond/test.diamond_blastp.daa - md5sum: d4a79ad1fcb2ec69460e5a09a9468db7 + md5sum: 0b539c68a5b66dd6e20ad5d218f4f4c6 - path: output/diamond/versions.yml diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf index d6d5a77a..d5949762 100644 --- a/tests/modules/diamond/blastx/main.nf +++ b/tests/modules/diamond/blastx/main.nf @@ -7,7 +7,7 @@ include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf' workflow test_diamond_blastx { - db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] outext = 'txt' @@ -17,7 +17,7 @@ workflow test_diamond_blastx { workflow test_diamond_blastx_daa { - db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] outext = 'daa' diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml index a2d35c80..9c30ba25 100644 --- a/tests/modules/diamond/blastx/test.yml +++ b/tests/modules/diamond/blastx/test.yml @@ -5,6 +5,7 @@ - diamond/blastx files: - path: output/diamond/test.diamond_blastx.txt + md5sum: eb2aebfa1cb42fcb2121c65528663307 - path: output/diamond/versions.yml - name: diamond blastx test_diamond_blastx_daa @@ -14,5 +15,5 @@ - diamond/blastx files: - path: output/diamond/test.diamond_blastx.daa - md5sum: 2a0ce0f7e01dcead828b87d5cbaccf7a + md5sum: 0df4a833408416f32981415873facc11 - path: output/diamond/versions.yml diff --git a/tests/modules/diamond/makedb/main.nf b/tests/modules/diamond/makedb/main.nf index 70982ae9..d309de6d 100644 --- a/tests/modules/diamond/makedb/main.nf +++ b/tests/modules/diamond/makedb/main.nf @@ -6,7 +6,7 @@ include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' workflow test_diamond_makedb { - input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ] DIAMOND_MAKEDB ( input ) } diff --git a/tests/modules/diamond/makedb/test.yml b/tests/modules/diamond/makedb/test.yml index c8f2d79e..cdddf735 100644 --- a/tests/modules/diamond/makedb/test.yml +++ b/tests/modules/diamond/makedb/test.yml @@ -1,8 +1,9 @@ - name: diamond makedb test_diamond_makedb - command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config -c ./tests/modules/diamond/makedb/nextflow.config + command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config tags: - - diamond - diamond/makedb + - diamond files: - - path: output/diamond/genome.fasta.dmnd - md5sum: 2447fb376394c20d43ea3aad2aa5d15d + - path: output/diamond/proteome.fasta.dmnd + md5sum: fc28c50b202dd7a7c5451cddff2ba1f4 + - path: output/diamond/versions.yml