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Bump DIAMOND version to 2.0.15

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James Fellows Yates 2022-04-29 21:05:12 +02:00
parent 7df2fae746
commit 39530b5ca7
10 changed files with 28 additions and 31 deletions
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8
modules/diamond/blastp/main.nf
View file

@ -2,12 +2,10 @@ process DIAMOND_BLASTP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

8
modules/diamond/blastx/main.nf
View file

@ -2,12 +2,10 @@ process DIAMOND_BLASTX {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
// singularity version higher than this at the current time.
conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

8
modules/diamond/makedb/main.nf
View file

@ -2,12 +2,10 @@ process DIAMOND_MAKEDB {
tag "$fasta" tag "$fasta"
label 'process_medium' label 'process_medium'
// Dimaond is limited to v2.0.9 because there is not a conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
// singularity version higher than this at the current time.
conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' : 'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }" 'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
input: input:
path fasta path fasta

1
tests/config/test_data.config
View file

@ -14,6 +14,7 @@ params {
genome_paf = "${test_data_dir}/genomics/sarscov2/genome/genome.paf" genome_paf = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes" genome_sizes = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
transcriptome_fasta = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta" transcriptome_fasta = "${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" transcriptome_paf = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed" test_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"

8
tests/modules/diamond/blastp/main.nf
View file

@ -7,8 +7,8 @@ include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf'
workflow test_diamond_blastp { workflow test_diamond_blastp {
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) ] fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
outext = 'txt' outext = 'txt'
DIAMOND_MAKEDB ( db ) DIAMOND_MAKEDB ( db )
@ -17,8 +17,8 @@ workflow test_diamond_blastp {
workflow test_diamond_blastp_daa { workflow test_diamond_blastp_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) ] fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
outext = 'daa' outext = 'daa'
DIAMOND_MAKEDB ( db ) DIAMOND_MAKEDB ( db )

8
tests/modules/diamond/blastp/test.yml
View file

@ -1,19 +1,19 @@
- name: diamond blastp test_diamond_blastp - name: diamond blastp test_diamond_blastp
command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
tags: tags:
- diamond
- diamond/blastp - diamond/blastp
- diamond
files: files:
- path: output/diamond/test.diamond_blastp.txt - path: output/diamond/test.diamond_blastp.txt
md5sum: 3ca7f6290c1d8741c573370e6f8b4db0 md5sum: 2515cf88590afa32356497e79a51fce9
- path: output/diamond/versions.yml - path: output/diamond/versions.yml
- name: diamond blastp test_diamond_blastp_daa - name: diamond blastp test_diamond_blastp_daa
command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
tags: tags:
- diamond
- diamond/blastp - diamond/blastp
- diamond
files: files:
- path: output/diamond/test.diamond_blastp.daa - path: output/diamond/test.diamond_blastp.daa
md5sum: d4a79ad1fcb2ec69460e5a09a9468db7 md5sum: 0b539c68a5b66dd6e20ad5d218f4f4c6
- path: output/diamond/versions.yml - path: output/diamond/versions.yml

4
tests/modules/diamond/blastx/main.nf
View file

@ -7,7 +7,7 @@ include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
workflow test_diamond_blastx { 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) ] fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
outext = 'txt' outext = 'txt'
@ -17,7 +17,7 @@ workflow test_diamond_blastx {
workflow test_diamond_blastx_daa { 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) ] fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
outext = 'daa' outext = 'daa'

3
tests/modules/diamond/blastx/test.yml
View file

@ -5,6 +5,7 @@
- diamond/blastx - diamond/blastx
files: files:
- path: output/diamond/test.diamond_blastx.txt - path: output/diamond/test.diamond_blastx.txt
md5sum: eb2aebfa1cb42fcb2121c65528663307
- path: output/diamond/versions.yml - path: output/diamond/versions.yml
- name: diamond blastx test_diamond_blastx_daa - name: diamond blastx test_diamond_blastx_daa
@ -14,5 +15,5 @@
- diamond/blastx - diamond/blastx
files: files:
- path: output/diamond/test.diamond_blastx.daa - path: output/diamond/test.diamond_blastx.daa
md5sum: 2a0ce0f7e01dcead828b87d5cbaccf7a md5sum: 0df4a833408416f32981415873facc11
- path: output/diamond/versions.yml - path: output/diamond/versions.yml

2
tests/modules/diamond/makedb/main.nf
View file

@ -6,7 +6,7 @@ include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
workflow test_diamond_makedb { 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 ) DIAMOND_MAKEDB ( input )
} }

9
tests/modules/diamond/makedb/test.yml
View file

@ -1,8 +1,9 @@
- name: diamond makedb test_diamond_makedb - 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: tags:
- diamond
- diamond/makedb - diamond/makedb
- diamond
files: files:
- path: output/diamond/genome.fasta.dmnd - path: output/diamond/proteome.fasta.dmnd
md5sum: 2447fb376394c20d43ea3aad2aa5d15d md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
- path: output/diamond/versions.yml