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Update MALT

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James Fellows Yates 2022-11-24 14:44:04 +01:00
parent f8b769a8f0
commit 9feb6c2db6
4 changed files with 6 additions and 8 deletions
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2
conf/modules.config
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@ -281,7 +281,7 @@ process {
} }
withName: MALT_RUN { withName: MALT_RUN {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
// one run with multiple samples, so fix ID to just db name to ensure clean log name // one run with multiple samples, so fix ID to just db name to ensure clean log name
ext.prefix = { "${meta.db_name}" } ext.prefix = { "${meta.db_name}" }
publishDir = [ publishDir = [

2
modules.json
View file

@ -107,7 +107,7 @@
}, },
"malt/run": { "malt/run": {
"branch": "master", "branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" "git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
}, },
"megan/rma2info": { "megan/rma2info": {
"branch": "master", "branch": "master",

8
modules/nf-core/malt/run/main.nf generated
View file

@ -2,14 +2,13 @@ process MALT_RUN {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.41" : null) conda (params.enable_conda ? "bioconda::malt=0.61" : 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/malt:0.41--1' : 'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
'quay.io/biocontainers/malt:0.41--1' }" 'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
input: input:
tuple val(meta), path(fastqs) tuple val(meta), path(fastqs)
val mode
path index path index
output: output:
@ -38,7 +37,6 @@ process MALT_RUN {
-o . \\ -o . \\
$args \\ $args \\
--inFile ${fastqs.join(' ')} \\ --inFile ${fastqs.join(' ')} \\
-m $mode \\
--index $index/ |&tee ${prefix}-malt-run.log --index $index/ |&tee ${prefix}-malt-run.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

2
subworkflows/local/profiling.nf
View file

@ -95,7 +95,7 @@ workflow PROFILING {
db: it[2] db: it[2]
} }
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db ) MALT_RUN ( ch_input_for_malt.reads, ch_input_for_malt.db )
ch_maltrun_for_megan = MALT_RUN.out.rma6 ch_maltrun_for_megan = MALT_RUN.out.rma6
.transpose() .transpose()