Custom Analysis Pipelines Tailored for Universal Reproducibility and Efficiency (CAPTURE) 1.0

Custom Analysis Pipelines Tailored for Universal Reproducibility and Efficiency (CAPTURE) 1.0 is a flexible bioinformatics framework for scaffolding the process of data analysis and reproducibility by project structure (i.e., directory structure), job execution, version control (i.e., Git, GitHub), data processing and analysis, results, environment standardization and documentation, and research product dissemination to the scientific community. CAPTURE 1.0 aims to address barriers to translational scientific progress by standardizing and automating computational rigor, reproducibility, and FAIR practices. Initial Public Release Add cap md5 command by @toniecrumley Add cap help command by @toniecrumley Add Megalinter to Github actions by @toniecrumley Add cap new command to create new CAPTURE projects by @toniecrumley Add cap run command by @toniecrumley Add cap md5 --slurm option by @toniecrumley Rename the lab-framework to CAPTURE by @toniecrumley in https://github.com/lasseignelab/capture/pull/1 Add cap update and version commands by @toniecrumley in https://github.com/lasseignelab/capture/pull/2 Add cap env command by @toniecrumley in https://github.com/lasseignelab/capture/pull/3 Add cap_data_link function by @toniecrumley in https://github.com/lasseignelab/capture/pull/4 Fix cap run environment override by @toniecrumley in https://github.com/lasseignelab/capture/pull/5 Add cap_data_download function by @toniecrumley in https://github.com/lasseignelab/capture/pull/6 Add cap_array_value function by @toniecrumley in https://github.com/lasseignelab/capture/pull/8 Make cap_data_download md5 error improvements by @toniecrumley in https://github.com/lasseignelab/capture/pull/9 Use most recent Bioconductor for Dockerfile by @toniecrumley in https://github.com/lasseignelab/capture/pull/10 Add --select and --ignore parameters to cap md5 by @toniecrumley in https://github.com/lasseignelab/capture/pull/11 Add tab completion to the CAPTURE cap command line by @toniecrumley in https://github.com/lasseignelab/capture/pull/14 Remove cap_data_download default unzip behavior by @tchowton in https://github.com/lasseignelab/capture/pull/15 Add processing of symlinks to cap md5 by @toniecrumley in https://github.com/lasseignelab/capture/pull/17 Add --normalize option to cap md5 by @toniecrumley in https://github.com/lasseignelab/capture/pull/16 Add -–subdirectory option to specify a subdirectory in cap_data_download by @tchowton in https://github.com/lasseignelab/capture/pull/18 Add cap_container function by @tchowton in https://github.com/lasseignelab/capture/pull/20 Rename bin/docker to bin/container by @tchowton in https://github.com/lasseignelab/capture/pull/24 Prevent script exit when a container exists by @toniecrumley in https://github.com/lasseignelab/capture/pull/26 Fix GitHub tests by @toniecrumley in https://github.com/lasseignelab/capture/pull/28 Add tests for cap run by @toniecrumley in https://github.com/lasseignelab/capture/pull/27 Add requirement for user to supply a tag for the dockerhub reference by @tchowton in https://github.com/lasseignelab/capture/pull/31 Fix run path issue for Slurm jobs by @tchowton in https://github.com/lasseignelab/capture/pull/38 Rename dockerfile to dockerfile-template by @tchowton in https://github.com/lasseignelab/capture/pull/36 Fix slurm error for files with parentheses in name by @toniecrumley in https://github.com/lasseignelab/capture/pull/42 Fix cap_container error with array jobs by @toniecrumley in https://github.com/lasseignelab/capture/pull/43 Add a Github pull request template by @toniecrumley in https://github.com/lasseignelab/capture/pull/47 Rename bin/conda to bin/env by @toniecrumley in https://github.com/lasseignelab/capture/pull/52 Add CAP_CONTAINER_TYPE to cap_container documentation by @toniecrumley in https://github.com/lasseignelab/capture/pull/51 Require commands to run from project root directory by @toniecrumley in https://github.com/lasseignelab/capture/pull/48 Add cap verify command by @toniecrumley in https://github.com/lasseignelab/capture/pull/13 Add job id to non-array Slurm job log file names by @toniecrumley in https://github.com/lasseignelab/capture/pull/54 Add -s,--slurm to cap run by @toniecrumley in https://github.com/lasseignelab/capture/pull/53 Add main branch tracking for cap new by @toniecrumley in https://github.com/lasseignelab/capture/pull/45 Add invalid environment name checking by @toniecrumley in https://github.com/lasseignelab/capture/pull/49 Show environment name for cap run by @toniecrumley in https://github.com/lasseignelab/capture/pull/50 Change license to GPL version 3 by @toniecrumley in https://github.com/lasseignelab/capture/pull/55 Add environment-specific improvements to cap env by @toniecrumley in https://github.com/lasseignelab/capture/pull/57 Add --source-file-name option to cap_data_download by @toniecrumley in https://github.com/lasseignelab/capture/pull/56 Fix cap run environment display when not using Slurm batch option by @toniecrumley in https://github.com/lasseignelab/capture/pull/60 Check the environment is valid for cap env command by @toniecrumley in https://github.com/lasseignelab/capture/pull/61 Version 1.0.0 by @toniecrumley in https://github.com/lasseignelab/capture/pull/59 New Contributors @toniecrumley made their first contribution in https://github.com/lasseignelab/capture/pull/1 @tchowton made their first contribution in https://github.com/lasseignelab/capture/pull/15 Full Changelog: https://github.com/lasseignelab/capture/compare/v0.0.1...v1.0.0