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Increase memory request for cell merge code.
A couple of runs ran out of memory with my original 1000 mb request.
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workflow/rules/star_solo_split.smk

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -158,7 +158,7 @@ rule merge_raw_cells:
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raw_unique_matrix = temp(SOLO_ROOT / get_gene_model() / "raw" / "matrix.mtx"),
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raw_em_matrix = temp(SOLO_ROOT / get_gene_model() / "raw" / "UniqueAndMult-EM.mtx"),
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resources:
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mem_mb = DEFAULT_MEM_MB
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mem_mb = 8192
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threads: 1
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run:
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from woldrnaseq.splitseq_merger import write_merged_splitseq_matrix
@@ -177,7 +177,7 @@ rule merge_sj_cells:
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sj_features = temp(SOLO_ROOT / "SJ" / "raw" / "features.tsv"),
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sj_matrix = temp(SOLO_ROOT / "SJ" / "raw" / "matrix.mtx"),
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resources:
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mem_mb = DEFAULT_MEM_MB
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mem_mb = 8192
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threads: 1
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run:
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from woldrnaseq.splitseq_merger import write_merged_splitseq_matrix
@@ -199,7 +199,7 @@ rule filter_merged_unique_cells:
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output_directory = lambda wildcards, output: Path(output.filtered_unique_matrix).parent,
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star_tmp = temp(directory("_STARtmp")),
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resources:
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mem_mb = DEFAULT_MEM_MB
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mem_mb = 8192
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threads: 1
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log: "filter_merged_unique_cells.out"
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singularity:

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