From 9a8a9c5a0929152f944f10be2e1ec1cef3c8da4a Mon Sep 17 00:00:00 2001 From: Anne Bertolini Date: Tue, 10 Oct 2023 16:55:40 +0200 Subject: [PATCH] [FEAT] After cellranger keep compressed and decompressed results --- workflow/rules/adt_cellranger.smk | 6 +++--- workflow/rules/adt_cellranger_no_hashing.smk | 6 +++--- workflow/rules/gex_cellranger.smk | 6 +++--- workflow/rules/gex_cellranger_no_hashing.smk | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/workflow/rules/adt_cellranger.smk b/workflow/rules/adt_cellranger.smk index aaa34f0..164edaa 100644 --- a/workflow/rules/adt_cellranger.smk +++ b/workflow/rules/adt_cellranger.smk @@ -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}' ; " diff --git a/workflow/rules/adt_cellranger_no_hashing.smk b/workflow/rules/adt_cellranger_no_hashing.smk index 8201e7f..f9f1a85 100644 --- a/workflow/rules/adt_cellranger_no_hashing.smk +++ b/workflow/rules/adt_cellranger_no_hashing.smk @@ -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}' ; " diff --git a/workflow/rules/gex_cellranger.smk b/workflow/rules/gex_cellranger.smk index a7c1641..693ad81 100644 --- a/workflow/rules/gex_cellranger.smk +++ b/workflow/rules/gex_cellranger.smk @@ -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}' ; " diff --git a/workflow/rules/gex_cellranger_no_hashing.smk b/workflow/rules/gex_cellranger_no_hashing.smk index 87edc76..672ee64 100644 --- a/workflow/rules/gex_cellranger_no_hashing.smk +++ b/workflow/rules/gex_cellranger_no_hashing.smk @@ -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}' ; "