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Fix MALT multiqc report clash

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This commit is contained in:
James Fellows Yates 2022-03-03 18:04:03 +01:00
parent 2c183ed2ed
commit e39c6a8ccb
4 changed files with 6 additions and 4 deletions
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2
modules.json
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@ -19,7 +19,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
"malt/run": { "malt/run": {
"git_sha": "76cdd46f3f8a77fb5023fb5a39c4ab99925b8b56" "git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
}, },
"multiqc": { "multiqc": {
"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"

3
modules/nf-core/modules/malt/run/main.nf generated
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@ -23,6 +23,7 @@ process MALT_RUN {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def avail_mem = 6 def avail_mem = 6
if (!task.memory) { if (!task.memory) {
log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@ -39,7 +40,7 @@ process MALT_RUN {
$args \\ $args \\
--inFile ${fastqs.join(' ')} \\ --inFile ${fastqs.join(' ')} \\
-m $mode \\ -m $mode \\
--index $index/ |&tee malt-run.log --index $index/ |&tee ${prefix}-malt-run.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

2
modules/nf-core/modules/malt/run/meta.yml generated
View file

@ -52,7 +52,7 @@ output:
- log: - log:
type: file type: file
description: Log of verbose MALT stdout description: Log of verbose MALT stdout
pattern: "malt-run.log" pattern: "*-malt-run.log"
authors: authors:
- "@jfy133" - "@jfy133"

3
workflows/taxprofiler.nf
View file

@ -203,7 +203,8 @@ workflow TAXPROFILER {
ch_versions = ch_versions.mix(MALT_RUN.out.versions.first()) ch_versions = ch_versions.mix(MALT_RUN.out.versions.first())
} }
// TODO MALT results overwriting per database?
// TODO Versions for Karken/MALT not report?
MULTIQC ( MULTIQC (
ch_multiqc_files.collect() ch_multiqc_files.collect()
) )