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49 Add filtering to merge module to exclude known failures #54

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merged 3 commits into from
May 30, 2024
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49 Add filtering to merge module to exclude known failures #54

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9cb25a2
Add branching for oversize
jashapiro May 30, 2024
7cc5f99
set a parameter for the max merge
jashapiro May 30, 2024
7b206c3
rename param
jashapiro May 30, 2024
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13 changes: 12 additions & 1 deletion modules/merge-sce/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@

// module parameters
params.reuse_merge = false
params.max_merge_libraries = 75 // maximum number of libraries to merge (current number is a guess, based on 59 working, but 104 not)
params.num_hvg = 2000 // number of HVGs to select

// merge workflow variables
Expand Down Expand Up @@ -131,13 +132,23 @@ workflow merge_sce {
def library_ids = processed_files.collect{it.name.replace('_processed.rds', '')}
return [project_id, library_ids, processed_files]
}
.branch{
// check the number of libraries
mergeable: it[1].size() < params.max_merge_libraries
oversized: true
}

project_branch.multiplexed
.subscribe{
log.warn("Not merging ${it[0]} because it contains multiplexed libraries.")
}

libraries_branch = libraries_ch
libraries_ch.oversized
.subscribe{
log.warn("Not merging ${it[0]} because it has too many libraries.")
}

libraries_branch = libraries_ch.mergeable
.branch{
has_merge: file("${publish_merge_base}/${it[0]}/${it[0]}_merged.rds").exists() && params.reuse_merge
make_merge: true
Expand Down