From fcefe167437cd8690ea8c8608a5df335e88c5afb Mon Sep 17 00:00:00 2001 From: David Williams Date: Fri, 8 Mar 2024 14:18:56 +0000 Subject: [PATCH] Prepended "outs" to filenames in cellranger extract --- cellranger_extract_rename/v1.0/rename_files.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cellranger_extract_rename/v1.0/rename_files.sh b/cellranger_extract_rename/v1.0/rename_files.sh index 0fd0cd9..485c976 100755 --- a/cellranger_extract_rename/v1.0/rename_files.sh +++ b/cellranger_extract_rename/v1.0/rename_files.sh @@ -174,7 +174,8 @@ if [[ $j -gt ${#linker_array[@]} || $j -lt 5 ]]; then exit 1 fi -file_list=(web_summary.html metrics_summary.csv raw_feature_bc_matrix.h5 possorted_genome_bam.bam possorted_genome_bam.bam.bai filtered_feature_bc_matrix.h5) +file_list=(outs/web_summary.html outs/metrics_summary.csv outs/raw_feature_bc_matrix.h5 outs/possorted_genome_bam.bam outs/possorted_genome_bam.bam.bai outs/filtered_feature_bc_matrix.h5) +# file_list=(web_summary.html metrics_summary.csv raw_feature_bc_matrix.h5 possorted_genome_bam.bam possorted_genome_bam.bam.bai filtered_feature_bc_matrix.h5) # file_list=(web_summary.html metrics_summary.csv raw_feature_bc_matrix.h5 possorted_genome_bam.bam possorted_genome_bam.bam.bai raw_feature_bc_matrix/matrix.mtx.gz raw_feature_bc_matrix/features.tsv.gz raw_feature_bc_matrix/barcodes.tsv.gz filtered_feature_bc_matrix/matrix.mtx.gz filtered_feature_bc_matrix/barcodes.tsv.gz filtered_feature_bc_matrix/features.tsv.gz) # Extracting and renaming files