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Remove custom params in GTDBTK/CLASSIFYWF #6651

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merged 4 commits into from
Sep 17, 2024
Merged

Remove custom params in GTDBTK/CLASSIFYWF #6651

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f6d3e9b
Use the proper version calling now implemented
jfy133 Sep 16, 2024
a77af8f
Remove custom params
jfy133 Sep 16, 2024
7a741c6
Fix test
jfy133 Sep 17, 2024
703327a
Merge branch 'master' into master
jfy133 Sep 17, 2024
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13 changes: 5 additions & 8 deletions modules/nf-core/gtdbtk/classifywf/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ process GTDBTK_CLASSIFYWF {
input:
tuple val(meta) , path("bins/*")
tuple val(db_name), path("database/*")
val use_pplacer_scratch_dir
path mash_db

output:
Expand All @@ -26,8 +27,8 @@ process GTDBTK_CLASSIFYWF {

script:
def args = task.ext.args ?: ''
def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
def pplacer_scratch = use_pplacer_scratch_dir ? "--scratch_dir pplacer_tmp" : ""
def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
prefix = task.ext.prefix ?: "${meta.id}"

"""
Expand All @@ -43,9 +44,7 @@ process GTDBTK_CLASSIFYWF {
--out_dir "\${PWD}" \\
--cpus ${task.cpus} \\
${mash_mode} \\
${pplacer_scratch} \\
--min_perc_aa ${params.gtdbtk_min_perc_aa} \\
--min_af ${params.gtdbtk_min_af}
${pplacer_scratch}

## If mash db given, classify/ and identify/ directories won't be created
if [[ -d classify/ && \$(ls -A classify/) ]]; then
Expand Down Expand Up @@ -74,8 +73,6 @@ process GTDBTK_CLASSIFYWF {
"""

stub:
def VERSION = '2.3.2'
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
prefix = task.ext.prefix ?: "${meta.id}"
"""
touch gtdbtk.${prefix}.stub.summary.tsv
Expand All @@ -90,7 +87,7 @@ process GTDBTK_CLASSIFYWF {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
gtdbtk: \$(echo "${VERSION}")
gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
END_VERSIONS
"""
}
3 changes: 3 additions & 0 deletions modules/nf-core/gtdbtk/classifywf/meta.yml
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Expand Up @@ -30,6 +30,9 @@ input:
type: file
description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy)
pattern: "*"
- use_pplacer_scratch_dir:
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type: boolean
description: Set to true to reduce pplacer memory usage by writing to disk (slower)
- mash_db:
type: file
description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
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Expand Up @@ -93,7 +93,7 @@
]
],
"9": [
"versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2"
"versions.yml:md5,2c94de2b8633b99e11881ab0193835d7"
],
"failed": [
[
Expand Down Expand Up @@ -176,7 +176,7 @@
]
],
"versions": [
"versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2"
"versions.yml:md5,2c94de2b8633b99e11881ab0193835d7"
],
"warnings": [
[
Expand All @@ -192,8 +192,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-03-26T09:39:21.632259941"
"timestamp": "2024-09-16T11:46:32.337929018"
}
}
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