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[FEAT] After cellranger keep compressed and decompressed results
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Anne Bertolini committed Oct 10, 2023
1 parent 4b79958 commit 9a8a9c5
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Showing 4 changed files with 12 additions and 12 deletions.
6 changes: 3 additions & 3 deletions workflow/rules/adt_cellranger.smk
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Expand Up @@ -76,9 +76,9 @@ rule cellranger_count_adt:
"{params.variousParams} "
"{params.targetCells}) "
"&> {log} "
"&& gunzip -c {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv.gz > {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv ; "
"gunzip -c {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz > {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv ; "
"gunzip -c {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz > {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx "
"&& gzip -dk {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv.gz ; "
"gzip -dk {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ; "
"gzip -dk {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz "
"&& ln -rs '{params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv' '{output.features_file}' ; "
"ln -rs '{params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx' '{output.matrix_file}' ; "
"ln -rs '{params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv' '{output.barcodes_file}' ; "
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6 changes: 3 additions & 3 deletions workflow/rules/adt_cellranger_no_hashing.smk
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Expand Up @@ -72,9 +72,9 @@ rule cellranger_count_adt:
"{params.variousParams} "
"{params.targetCells}) "
"&> {log} "
"&& gunzip -c {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv.gz > {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv ; "
"gunzip -c {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz > {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv ; "
"gunzip -c {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz > {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx "
"&& gzip -dk {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv.gz ; "
"gzip -dk {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ; "
"gzip -dk {params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz "
"&& ln -rs '{params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/features.tsv' '{output.features_file}' ; "
"ln -rs '{params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/matrix.mtx' '{output.matrix_file}' ; "
"ln -rs '{params.cr_out}{params.sample}/outs/filtered_feature_bc_matrix/barcodes.tsv' '{output.barcodes_file}' ; "
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6 changes: 3 additions & 3 deletions workflow/rules/gex_cellranger.smk
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Expand Up @@ -47,9 +47,9 @@ rule cellranger_count_gex:
"--localcores={threads} "
"{params.variousParams}) "
"&> {log} ; "
"gunzip {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/features.tsv.gz ; "
"gunzip {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ; "
"gunzip {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz ; "
"gzip -dk {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/features.tsv.gz ; "
"gzip -dk {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ; "
"gzip -dk {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz ; "
"ln -frs '{params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/features.tsv' '{output.features_file}' ; "
"ln -frs '{params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/matrix.mtx' '{output.matrix_file}' ; "
"ln -frs '{params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/barcodes.tsv' '{output.barcodes_file}' ; "
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6 changes: 3 additions & 3 deletions workflow/rules/gex_cellranger_no_hashing.smk
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Expand Up @@ -51,9 +51,9 @@ rule cellranger_count_gex:
"--localcores={threads} "
"{params.variousParams}) "
"&> {log} ; "
"gunzip {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/features.tsv.gz ; "
"gunzip {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ; "
"gunzip {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz ; "
"gzip -dk {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/features.tsv.gz ; "
"gzip -dk {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ; "
"gzip -dk {params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/matrix.mtx.gz ; "
"ln -frs '{params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/features.tsv' '{output.features_file}' ; "
"ln -frs '{params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/matrix.mtx' '{output.matrix_file}' ; "
"ln -frs '{params.cr_out}{params.mySample}/outs/filtered_feature_bc_matrix/barcodes.tsv' '{output.barcodes_file}' ; "
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