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Fix MALT multiqc report clash
This commit is contained in:
parent
2c183ed2ed
commit
e39c6a8ccb
4 changed files with 6 additions and 4 deletions
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@ -19,7 +19,7 @@
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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"malt/run": {
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"malt/run": {
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"git_sha": "76cdd46f3f8a77fb5023fb5a39c4ab99925b8b56"
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"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
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},
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},
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"multiqc": {
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"multiqc": {
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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3
modules/nf-core/modules/malt/run/main.nf
generated
3
modules/nf-core/modules/malt/run/main.nf
generated
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@ -23,6 +23,7 @@ process MALT_RUN {
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script:
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def avail_mem = 6
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def avail_mem = 6
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if (!task.memory) {
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if (!task.memory) {
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log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
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log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
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@ -39,7 +40,7 @@ process MALT_RUN {
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$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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-m $mode \\
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--index $index/ |&tee malt-run.log
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--index $index/ |&tee ${prefix}-malt-run.log
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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2
modules/nf-core/modules/malt/run/meta.yml
generated
2
modules/nf-core/modules/malt/run/meta.yml
generated
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@ -52,7 +52,7 @@ output:
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- log:
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- log:
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type: file
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type: file
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description: Log of verbose MALT stdout
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description: Log of verbose MALT stdout
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pattern: "malt-run.log"
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pattern: "*-malt-run.log"
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authors:
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authors:
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- "@jfy133"
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- "@jfy133"
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@ -203,7 +203,8 @@ workflow TAXPROFILER {
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ch_versions = ch_versions.mix(MALT_RUN.out.versions.first())
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ch_versions = ch_versions.mix(MALT_RUN.out.versions.first())
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}
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}
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// TODO MALT results overwriting per database?
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// TODO Versions for Karken/MALT not report?
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MULTIQC (
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MULTIQC (
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ch_multiqc_files.collect()
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ch_multiqc_files.collect()
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)
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)
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