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Add process for converting merged objects to AnnData #613

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merged 6 commits into from
Dec 14, 2023
Merged

Add process for converting merged objects to AnnData #613

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8fccf4a
add process for converting to anndata
allyhawkins Dec 8, 2023
6e04a58
Merge remote-tracking branch 'origin/development' into allyhawkins/me…
allyhawkins Dec 11, 2023
b2cdc19
Merge branch 'development' into allyhawkins/merged-sce-to-anndata
allyhawkins Dec 14, 2023
9b745e6
use correct include_altexp arg
allyhawkins Dec 14, 2023
ba9ae7b
use scpcaTools:edge
allyhawkins Dec 14, 2023
b93c5d0
some missed syntax and merge_groups
allyhawkins Dec 14, 2023
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4 changes: 2 additions & 2 deletions bin/merge_sces.R
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ option_list <- list(
the default is n_hvg = 2000"
),
make_option(
opt_str = c("--include_alt_exp"),
opt_str = c("--include_altexp"),
action = "store_true",
default = FALSE,
help = "Keep any altExp present in the merged object."
Expand Down Expand Up @@ -115,7 +115,7 @@ merged_sce <- scpcaTools::merge_sce_list(
batch_column = "library_id",
preserve_rowdata_cols = "gene_symbol",
cell_id_column = "cell_id",
include_alt_exp = include_alt_exp
include_altexp = opt$include_altexp
)


Expand Down
2 changes: 1 addition & 1 deletion config/containers.config
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@@ -1,5 +1,5 @@
// Docker container images
SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:v0.3.1'
SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:edge'

ALEVINFRY_CONTAINER = 'quay.io/biocontainers/alevin-fry:0.7.0--h9f5acd7_1'
BCFTOOLS_CONTAINER = 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0'
Expand Down
37 changes: 36 additions & 1 deletion merge.nf
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Expand Up @@ -46,7 +46,7 @@ process merge_sce {
--input_sce_files "${input_sces}" \
--output_sce_file "${merged_sce_file}" \
--n_hvg ${params.num_hvg} \
"${has_adt ? "--include_alt_exp" : ''} \
${has_adt ? "--include_altexp" : ''} \
--threads ${task.cpus}
"""
stub:
Expand Down Expand Up @@ -85,6 +85,38 @@ process merge_report {
"""
}

process export_anndata{
container params.SCPCATOOLS_CONTAINER
label 'mem_16'
tag "${merge_group}"
publishDir "${params.results_dir}/merged/${merge_group}", mode: 'copy'
input:
tuple val(merge_group), val(has_adt), path(merged_sce_file)
output:
tuple val(merge_group), path("${merge_group}_merged_*.hdf5")
script:
rna_hdf5_file = "${merge_group}_merged_rna.hdf5"
feature_hdf5_file = "${merge_group}_merged_adt.hdf5"
"""
sce_to_anndata.R \
--input_sce_file ${merged_sce_file} \
--output_rna_h5 ${rna_hdf5_file} \
--output_feature_h5 ${feature_hdf5_file} \
${has_adt ? "--feature_name adt" : ''}

# move normalized counts to X in AnnData
move_counts_anndata.py --anndata_file ${rna_hdf5_file}
${has_adt ? "move_counts_anndata.py --anndata_file ${feature_hdf5_file}" : ''}
"""
stub:
rna_hdf5_file = "${merge_group}_merged_rna.hdf5"
feature_hdf5_file = "${merge_group}_merged_adt.hdf5"
"""
touch ${rna_hdf5_file}
${has_adt ? "touch ${feature_hdf5_file}" : ''}
"""
}

workflow {

// grab project ids to run
Expand Down Expand Up @@ -129,4 +161,7 @@ workflow {

// TODO: generate merge report
//merge_report(merge_sce.out, file(merge_template))

// export merged objects to AnnData
export_anndata(merge_sce.out)
}