Merge branch 'RTIInternational:master' into master

cellranger_extract_rename/v1.0/Dockerfile → cellranger_extract_rename/v1.1/Dockerfile

@@ -1,11 +1,12 @@
-FROM joshkeegan/zip:3.19.1
+FROM alpine:3.20.3
 
 LABEL maintainer="David Williams <[email protected]>"
-LABEL description="This Docker image contains an in-house script written to extract and rename files coming from the 'outs.zip' file from Cellranger"
+LABEL description="This Docker image contains an in-house script written to extract and rename files coming from the 'outs.zip' file or outs directory from Cellranger"
+LABEL software-version="1.1"
 
 RUN apk update
-RUN apk add vim vim-doc vim-tutor
-RUN apk add bash
+RUN apk add --no-cache vim vim-doc vim-tutor zip unzip
+RUN apk add --no-cache bash
 
 # Add scripts to make it run
 ADD rename_files.sh /

cellranger_extract_rename/v1.0/README.md → cellranger_extract_rename/v1.1/README.md

@@ -1,6 +1,6 @@
 # Description
 
-This Docker image contains an in-house script written to extract and rename key files from the large 'outs.zip' file from the Cell Ranger process.  Its purpose is to fit in the single cell RNA sequencing workflow, as well as ATACseq and potentially GUIDEseq, in the RMIP project.  The Input to this should be ZIP file(s) coming from a Cell Ranger run, and the output is an output directory with renamed files and a renamed copy of the input 'outs.zip' file.  Files and relative paths within the 'outs.zip' file are listed in the table below:
+This Docker image contains an in-house script written to extract and rename key files from the large 'outs.zip' file or large 'outs' directory from the Cell Ranger process.  Its purpose is to fit in the single cell RNA sequencing workflow, as well as ATACseq and potentially GUIDEseq, in the RMIP project.  The Input to this should be a ZIP file or directory coming from a Cell Ranger run, and the output is an output directory with renamed files and a renamed copy of the input 'outs.zip' file (if given).  Files and relative paths within the 'outs.zip' file are listed in the table below:
 
 | Directory | Filename | Description | Link |
 | -- | -- | -- | -- |
@@ -11,53 +11,54 @@ This Docker image contains an in-house script written to extract and rename key
 | ./ | possorted_genome_bam.bam.bai | Index file associated with the BAM file. | https://www.10xgenomics.com/support/software/cell-ranger/analysis/outputs/cr-outputs-bam |
 | ./ | filtered_feature_bc_matrix.h5 | Filtered feature-barcode matrices describing the number of UMIs associated with a feature and a barcode. | https://www.10xgenomics.com/support/software/cell-ranger/analysis/outputs/cr-outputs-h5-matrices |
 
-Each of these files are copied to an output directory and prepended with a "linker" for a given sample.  Additionally, the given ZIP file is copied to this directory and also prepended with this linker.  Given the example linker `RMIP_001_002_A_003_B`, this can be separated into different components, delimited by `_`.  Details on the linker and its format are below.
+Each of these files are copied to an output directory and prepended with a "linker" for a given sample.  Additionally, the given ZIP file is copied to this directory and also prepended with this linker.  Given the example linker `RMIP_001_allo2_A_003_B`, this can be separated into different components, delimited by `_`.  Details on the linker and its format are below.
 
 | Name | Component | Description |
 | -- | -- | -- |
 |  RMIP identifier | `RMIP` | Goes at the beginning of each linker |
 |  Project Identifier | `001` | Numeric only |
-|  Participant ID | `002` | Alphanumeric only, no length restrictions |
+|  Participant ID | `allo2` | Alphanumeric only, no length restrictions |
 |  Discriminator | `A` | Alphabetic only - combination with "Identifier" uniquely identifies every collection event |
 |  Identifier | `003` | Numeric only - combination with "Discriminator" uniquely identifies every collection event |
 |  Vial identifier (alphabetic) | `B` | Alphabetic only - identifies specific collection aliquot - optional if only one vial |
 
 ## Sample usage
 
-This script is used to extract results from the large output ZIP file from Cell Ranger.
+This script is used to extract results from the output of a Cell Ranger run.
 
 Build
 ```
-docker build -t cellranger_extract_rename:v1 .
+docker build -t cellranger_extract_rename:v1.1 .
 ```
 
 Run
 ```
-docker run -it -v $PWD:/data cellranger_extract_rename:v1 rename_files.sh
+docker run -it -v $PWD:/data cellranger_extract_rename:v1.1 rename_files.sh
 ```
 
 Usage info:
 ```
-Usage: ./rename_files.sh [OPTIONS]
+Usage: /rename_files.sh [OPTIONS]
 Options:
  -h, --help         Display this help message
  -v, --verbose      Enable verbose mode
- -l, --linker       STRING Specify name of linker to prepend to extracted files (format 'RMIP_<ddd>_<ddd>_<w>_<ddd>_<w>') - Required
-                       e.g. linker='RMIP_001_001_A_001_A'
+ -l, --linker       STRING Specify name of linker to prepend to extracted files (format 'RMIP_<ddd>_<alphanum>_<w>_<ddd>_<w>') - Required
+                       e.g. linker='RMIP_001_allo1_A_001_A'
                        Note that the Vial Identifier (last letter) is optional
- -z, --zip_file     STRING/PATH Specify name and path of ZIP file to read, decompress, and rename - Required
+ -i, --input        STRING/PATH Specify name and path of either ZIP file to read OR input directory - Required
  -o, --output_dir   STRING/PATH Specify directory where to put extracted files.  Default = '.'
 
 Example usage
- Required flags:               ./rename_files.sh -z outs.zip -l RMIP_001_001_A_001_A
- Verbose mode:                 ./rename_files.sh -v -z outs.zip -l RMIP_001_001_A_001_B
- Writing to output directory:  ./rename_files.sh -z outs.zip -l RMIP_001_001_A_001_C -o test_output
+ Required flags (ZIP input):               ./rename_files.sh -i outs.zip -l RMIP_001_allo1_A_001_A
+ Required flags (DIRECTORY input):         ./rename_files.sh -i outs -l RMIP_001_allo1_A_001_B
+ Writing to output directory:              ./rename_files.sh -i outs.zip -l RMIP_001_allo1_A_001_C -o outs
+ Verbose mode:                             ./rename_files.sh -v -i outs.zip -l RMIP_001_allo1_A_001_D
 ```
 
 ## Files included
 
 - `Dockerfile`: the Docker file used to build this image
-- `rename_files.sh`: Bash shell script that serves as the main executable when the Docker container is run.  Expected behavior is to take a specified input ZIP file in the current working directory, unzip specific files from it, and rename those files to include a prefix signifying a sample name.  This writes those specific files and a renamed copy of the given ZIP file to an output directory.
+- `rename_files.sh`: Bash shell script that serves as the main executable when the Docker container is run.  Expected behavior is to take a specified input ZIP file OR directory in the current working directory, extract specific files from it, and rename those files to include a prefix signifying a sample name.  This writes those specific files and a renamed copy of the ZIP file (if given) to an output directory.
 
 ## Contact