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Migrate CAT local modules to nf-core ones #799

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Merged
dialvarezs merged 27 commits into from
Jun 2, 2025
Merged

Migrate CAT local modules to nf-core ones #799

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ed1a688
Install CAT nf-core modules
dialvarezs May 9, 2025
c707291
Merge remote-tracking branch 'upstream/dev' into dev-cat
dialvarezs May 12, 2025
efe5a28
CAT basic functionality
dialvarezs May 15, 2025
3590c25
Merge remote-tracking branch 'upstream/dev' into dev-cat
dialvarezs May 15, 2025
edb8986
[automated] Fix code linting
nf-core-bot May 16, 2025
5446a47
Implement cat post classification steps
dialvarezs May 19, 2025
47305bf
Prettier
dialvarezs May 19, 2025
a75b50b
Merge remote-tracking branch 'origin/dev-cat' into dev-cat
dialvarezs May 19, 2025
1583563
Integrate cat/download and cat/prepare, old module cleanup
dialvarezs May 22, 2025
2693fa2
Final implementation fixes
dialvarezs May 23, 2025
2e45cf0
Merge remote-tracking branch 'upstream/dev' into dev-cat
dialvarezs May 23, 2025
24813cc
Update changelog and docs, add new param to enable run cat on unbinne…
dialvarezs May 23, 2025
66ae486
Linting fixes
dialvarezs May 23, 2025
d3472e9
Fix dir db channel, simplify resource configs
dialvarezs May 25, 2025
110447d
Add commentaries for catpack/bins and catpack/contigs inputs
dialvarezs May 25, 2025
f150bf3
Update modules
dialvarezs May 25, 2025
bd366e7
Merge branch 'dev' into dev-cat
jfy133 May 27, 2025
c62663d
Update CHANGELOG.md
jfy133 May 27, 2025
ef9689f
Apply suggestions from code review
dialvarezs May 27, 2025
b6e03e0
Merge remote-tracking branch 'upstream/dev' into dev-cat
dialvarezs May 27, 2025
40806ff
Apply more suggestions from review
dialvarezs May 27, 2025
88ca2ec
Merge branch 'dev' into dev-cat
jfy133 May 28, 2025
f93c3fe
Add cat bin summary and change official taxonomy parameter
dialvarezs May 30, 2025
27b2546
Merge remote-tracking branch 'upstream/dev' into dev-cat
dialvarezs May 30, 2025
5b9902e
Update changelog and output
dialvarezs May 30, 2025
21b3ed6
Apply suggestions from code review
dialvarezs Jun 1, 2025
b676d93
Update nextflow_schema.json
dialvarezs Jun 2, 2025
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Fix dir db channel, simplify resource configs
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@dialvarezs
dialvarezs committed May 25, 2025
commit d3472e97ed6a98bf6a965db41b9301e7ae4441dd
14 changes: 1 addition & 13 deletions conf/base.config
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Expand Up @@ -104,23 +104,11 @@ process {
memory = { 20.GB * task.attempt }
time = { 12.h * task.attempt }
}
withName: CATPACK_DOWNLOAD {
time = { 12.h * task.attempt }
}
withName: CATPACK_PREPARE {
cpus = { 10 * task.attempt }
memory = { 200.GB * task.attempt }
time = { 16.h * task.attempt }
}
withName: CATPACK_BINS {
cpus = { 10 * task.attempt }
memory = { 120.GB * task.attempt }
time = { 12.h * task.attempt }
}
withName: CATPACK_CONTIGS {
cpus = { 10 * task.attempt }
memory = { 120.GB * task.attempt }
time = { 12.h * task.attempt }
memory = { 60.GB * task.attempt }
}
withName: GTDBTK_CLASSIFYWF {
cpus = { 10 * task.attempt }
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1 change: 1 addition & 0 deletions subworkflows/local/catpack.nf
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Expand Up @@ -34,6 +34,7 @@ workflow CATPACK {
else {
ch_cat_db_dir = Channel.fromPath(params.cat_db, checkIfExists: true, type: 'dir')
.map { dir -> [[id: 'cat_db'], dir] }
.first()
}

ch_cat_db = ch_cat_db_dir.multiMap { meta, dir ->
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