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Update MALT
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parent
f8b769a8f0
commit
9feb6c2db6
4 changed files with 6 additions and 8 deletions
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@ -281,7 +281,7 @@ process {
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}
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}
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withName: MALT_RUN {
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}" }
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ext.prefix = { "${meta.db_name}" }
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publishDir = [
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publishDir = [
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@ -107,7 +107,7 @@
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},
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},
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"malt/run": {
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"malt/run": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
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},
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},
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"megan/rma2info": {
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"megan/rma2info": {
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"branch": "master",
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"branch": "master",
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8
modules/nf-core/malt/run/main.nf
generated
8
modules/nf-core/malt/run/main.nf
generated
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@ -2,14 +2,13 @@ process MALT_RUN {
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tag "$meta.id"
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tag "$meta.id"
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label 'process_high'
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label 'process_high'
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conda (params.enable_conda ? "bioconda::malt=0.41" : null)
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conda (params.enable_conda ? "bioconda::malt=0.61" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
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'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
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'quay.io/biocontainers/malt:0.41--1' }"
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'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
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input:
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input:
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tuple val(meta), path(fastqs)
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tuple val(meta), path(fastqs)
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val mode
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path index
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path index
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output:
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output:
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@ -38,7 +37,6 @@ process MALT_RUN {
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-o . \\
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-o . \\
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$args \\
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$args \\
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--inFile ${fastqs.join(' ')} \\
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--inFile ${fastqs.join(' ')} \\
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-m $mode \\
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--index $index/ |&tee ${prefix}-malt-run.log
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--index $index/ |&tee ${prefix}-malt-run.log
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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@ -95,7 +95,7 @@ workflow PROFILING {
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db: it[2]
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db: it[2]
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}
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}
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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MALT_RUN ( ch_input_for_malt.reads, ch_input_for_malt.db )
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ch_maltrun_for_megan = MALT_RUN.out.rma6
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ch_maltrun_for_megan = MALT_RUN.out.rma6
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.transpose()
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.transpose()
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