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update: MALT build version bump (#699)

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* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Bump versions

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
James A. Fellows Yates 2021-09-15 17:46:29 +02:00 committed by GitHub
parent 26fc617983
commit 561f16fe74
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2 changed files with 7 additions and 9 deletions
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8
modules/malt/build/main.nf
View file

@ -11,13 +11,11 @@ process MALT_BUILD {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
// Do not **auto-bump** due to problem with change of version numbering between 0.4.1 and 0.5.2 conda (params.enable_conda ? "bioconda::malt=0.53" : null)
// (originally 0.4.1 was listed as 0.41, so is always selected as 'latest' even though it is not!)
conda (params.enable_conda ? "bioconda::malt=0.5.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0" container "https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0"
} else { } else {
container "quay.io/biocontainers/malt:0.5.2--0" container "quay.io/biocontainers/malt:0.53--hdfd78af_0"
} }
input: input:

8
tests/modules/malt/build_test/test.yml
View file

@ -17,9 +17,9 @@
- path: output/malt/malt_index/taxonomy.idx - path: output/malt/malt_index/taxonomy.idx
md5sum: bb335e7c378a5bd85761b6eeed16d984 md5sum: bb335e7c378a5bd85761b6eeed16d984
- path: output/malt/malt_index/taxonomy.map - path: output/malt/malt_index/taxonomy.map
md5sum: ae2ea08b2119eba932a9cbcd9e634917 md5sum: f6b05bbab2149e388cb769098e14d433
- path: output/malt/malt_index/taxonomy.tre - path: output/malt/malt_index/taxonomy.tre
md5sum: 511ec8ff4fd8aaa20d59b5a91ed4e852 md5sum: bde26a1fff5c63d3046d3863607a1e70
- name: malt build gff - name: malt build gff
command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build_gff -c tests/config/nextflow.config command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build_gff -c tests/config/nextflow.config
tags: tags:
@ -43,6 +43,6 @@
- path: output/malt/malt_index/taxonomy.idx - path: output/malt/malt_index/taxonomy.idx
md5sum: bb335e7c378a5bd85761b6eeed16d984 md5sum: bb335e7c378a5bd85761b6eeed16d984
- path: output/malt/malt_index/taxonomy.map - path: output/malt/malt_index/taxonomy.map
md5sum: ae2ea08b2119eba932a9cbcd9e634917 md5sum: f6b05bbab2149e388cb769098e14d433
- path: output/malt/malt_index/taxonomy.tre - path: output/malt/malt_index/taxonomy.tre
md5sum: 511ec8ff4fd8aaa20d59b5a91ed4e852 md5sum: bde26a1fff5c63d3046d3863607a1e70