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Bump Nextclade version to 1.10.1 (#1236)

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Harshil Patel 2022-01-27 12:53:14 +00:00 committed by GitHub
parent fc1e694e6e
commit d70526c806
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6 changed files with 18 additions and 14 deletions
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6
modules/nextclade/datasetget/main.nf
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@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET {
tag "$dataset" tag "$dataset"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null) conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : 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/nextclade:1.9.0--h9ee0642_0' : 'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }" 'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
input: input:
val dataset val dataset

6
modules/nextclade/run/main.nf
View file

@ -2,10 +2,10 @@ process NEXTCLADE_RUN {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null) conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : 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/nextclade:1.9.0--h9ee0642_0' : 'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }" 'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

3
tests/modules/nextclade/datasetget/main.nf
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@ -8,7 +8,8 @@ workflow test_nextclade_datasetget {
dataset = 'sars-cov-2' dataset = 'sars-cov-2'
reference = 'MN908947' reference = 'MN908947'
tag = '2022-01-05T19:54:31Z' tag = '2022-01-18T12:00:00Z'
NEXTCLADE_DATASETGET ( dataset, reference, tag ) NEXTCLADE_DATASETGET ( dataset, reference, tag )
} }

8
tests/modules/nextclade/datasetget/test.yml
View file

@ -9,12 +9,14 @@
- path: output/nextclade/sars-cov-2/primers.csv - path: output/nextclade/sars-cov-2/primers.csv
md5sum: 5990c3483bf66ce607aeb90a44e7ef2e md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
- path: output/nextclade/sars-cov-2/qc.json - path: output/nextclade/sars-cov-2/qc.json
md5sum: 018fa0c0b0d2e824954e37e01495d549 md5sum: c512f51fda0212b21ffff05779180963
- path: output/nextclade/sars-cov-2/reference.fasta - path: output/nextclade/sars-cov-2/reference.fasta
md5sum: c7ce05f28e4ec0322c96f24e064ef55c md5sum: c7ce05f28e4ec0322c96f24e064ef55c
- path: output/nextclade/sars-cov-2/sequences.fasta - path: output/nextclade/sars-cov-2/sequences.fasta
md5sum: 41129d255b99e0e92bdf20e866b99a1b md5sum: 41129d255b99e0e92bdf20e866b99a1b
- path: output/nextclade/sars-cov-2/tag.json - path: output/nextclade/sars-cov-2/tag.json
md5sum: 2f6d8e806d9064571ee4188ef1304c9c md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
- path: output/nextclade/sars-cov-2/tree.json - path: output/nextclade/sars-cov-2/tree.json
md5sum: f8fb33ed62b59142ac20998eb599df6c md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
- path: output/nextclade/sars-cov-2/virus_properties.json
md5sum: 5f2de3949e07cb633f3d9e4a7654dc81

3
tests/modules/nextclade/run/main.nf
View file

@ -9,7 +9,7 @@ workflow test_nextclade_run {
dataset = 'sars-cov-2' dataset = 'sars-cov-2'
reference = 'MN908947' reference = 'MN908947'
tag = '2022-01-05T19:54:31Z' tag = '2022-01-18T12:00:00Z'
NEXTCLADE_DATASETGET ( dataset, reference, tag ) NEXTCLADE_DATASETGET ( dataset, reference, tag )
@ -20,3 +20,4 @@ workflow test_nextclade_run {
NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset ) NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
} }

6
tests/modules/nextclade/run/test.yml
View file

@ -6,8 +6,8 @@
files: files:
- path: output/nextclade/test.json - path: output/nextclade/test.json
- path: output/nextclade/test.csv - path: output/nextclade/test.csv
md5sum: 3b87a4da190ba2e1fdc8418dc3a7ffdb md5sum: 570c1aa2d5fd25c23d0042c1b06108e1
- path: output/nextclade/test.tsv - path: output/nextclade/test.tsv
md5sum: 449393288e8734a02def139c550a8d9b md5sum: dd76e1a4c760785489be4e4a860b4d00
- path: output/nextclade/test.tree.json - path: output/nextclade/test.tree.json
md5sum: 9c6e33cb7ff860bee6194847bd2c855c md5sum: 3591b4dc1542995a7ffcffcb1f52b524