# buisciii-tools
[](https://github.com/BU-ISCIII/buisciii-tools/actions/workflows/python_lint.yml)
[](https://github.com/psf/black)
BU-ISCIII provides a serie or services in its portfolio for supporting bioinformatics analysis to the labs in the Institute of Health Carlos III. bu-isciii tools is a set of helper tools for management of these bioinformatics analysis together with the LIMS ([iSkyLIMS](https://github.com/BU-ISCIII/iSkyLIMS))
- [buisciii-tools](#buisciii-tools)
- [Installation](#installation)
- [Micromamba and pip](#micromamba-and-pip)
- [Dev version](#dev-version)
- [Usage](#usage)
- [Command-line](#command-line)
- [list](#list)
- [new-service](#new-service)
- [scratch](#scratch)
- [Finish](#finish)
- [clean](#clean)
- [scratch back](#scratch-back)
- [copy\_sftp](#copy_sftp)
- [bioinfo\_doc](#bioinfo_doc)
- [archive](#archive)
- [autoclean\_sftp](#autoclean_sftp)
- [fix-permissions](#fix-permissions)
- [Acknowledgements](#acknowledgements)
## Installation
### Micromamba and pip
```bash
micromamba create -n buisciii -f environment.yml
micromamba activate buisciii
pip install buisciii-tools
```
or
```bash
git checkout main
conda create -n buisciii -f environment.yml
conda activate
pip install buisciii-tools
```
### Dev version
If you want to install the latest code in the repository:
```bash
micromamba create -n buisciii_dev -f environment.yml
micromamba activate buisciii_dev
pip install --force-reinstall --upgrade git+https://github.com/bu-isciii/buisciii-tools.git@develop
```
or locally:
```bash
git checkout develop
micromamba create -n buisciii_dev -f environment.yml
micromamba activate buisciii_dev
pip install .
```
## Usage
### Command-line
Run bu-isciii tools:
```bash
bu-isciii --help
```
Outputs the following:
```bash
Usage: bu-isciii [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
-v, --verbose Print verbose output to the console.
-l, --log-file <filename> Save a verbose log to a file.
-u, --api_user TEXT User for the API logging
-p, --api_password TEXT Password for the API logging
-c, --cred_file TEXT Config file with API logging credentials
--help Show this message and exit
Commands:
list List available bu-isciii services.
clean Service cleaning.
new-service Create new service, it will create folder and copy...
scratch Copy service folder to scratch directory for execution.
copy-sftp Copy resolution FOLDER to sftp, change status of...
finish Service cleaning, remove big files, rename folders before...
bioinfo-doc Create the folder documentation structure in bioinfo_doc...
archive Archive services or retrieve services from archive
autoclean-sftp Clean old sftp services
fix-permissions Fix permissions
```
#### list
List available bu-isciii services:
```bash
bu-isciii list
```
Help:
```bash
Usage: bu-isciii list [OPTIONS] <service>
List available bu-isciii services.
Options:
--help Show this message and exit.
```
Output:
```bash
┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Service name ┃ Description ┃ Github ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ assembly_annotation │ Nextflow assembly pipeline to assemble │ https://github.com/Daniel-VM/bacass/... │
│ │ bacterial genomes │ │
│ mtbseq_assembly │ Mycobacterium tuberculosis mapping, │ https://github.com/ngs-fzb/MTBseq_source │
│ │ variant calling and detection of │ │
│ │ resistance using MTBseq │ │
│ mtbseq │ Mycobacterium tuberculosis mapping, │ https://github.com/ngs-fzb/MTBseq_source │
│ │ variant calling and detection of │ │
│ │ resistance using MTBseq │ │
│ pikavirus │ PikaVirus, a mapping-based tool for │ https://github.com/BU-ISCIII/PikaVirus │
│ │ metagenome analysis of virus. │ │
│ plasmidid_assembly │ Plasmid identification tool based on │ https://github.com/BU-ISCIII/plasmidID │
│ │ mapping and assisted by assembly │ │
│ wgmlst_taranis │ Multilocus sequence typing (MLST) using │ https://github.com/BU-ISCIII/taranis │
│ │ Taranis │ │
│ wgmlst_chewbbaca │ Multilocus sequence typing (MLST) using │ https://github.com/B-UMMI/chewBBACA │
│ │ chewBBACA │ │
│ viralrecon │ Viral genome reconstruction analysis for │ https://github.com/BU-ISCIII/viralrecon │
│ │ SARS-COV-2 data │ │
│ rnaseq │ RNA-seq analysis │ https://github.com/nf-core/rnaseq │
│ lowfreq_panel │ Low frequency variant calling from │ │
│ │ enrichment panel. │ │
│ snippy │ Rapid haploid variant calling and core │ https://github.com/tseemann/snippy │
│ │ genome alignment │ │
│ seek_and_destroy │ Simple pipeline for basic quality │ https://github.com/GuilleGorines/Seek-Des… │
│ │ control, host removal and exploratory │ │
│ │ analysis of samples. │ │
│ ariba_characterization │ │ │
│ mag_met │ 1- Bioinformatics best-practise analysis │ https://github.com/nf-core/mag or │
│ │ for taxonomic classification and │ https://github.com/nf-core/taxprofiler │
│ │ profiling; 2- Bioinformatics best-practise│ │
│ │ analysis pipeline for assembly, binning │ │
└────────────────────────┴───────────────────────────────────────────┴────────────────────────────────────────────┘
```
#### new-service
Example of usage:
```bash
bu-isciii new-service <resolution_id>
```
Help:
```bash
Usage: bu-isciii new-service [OPTIONS] <resolution id>
Create new service, it will create folder and copy template depending on
selected service.
Options:
-p, --path PATH Path to create the service folder
-n, --no_create_folder No create service folder, only resolution
-a, --ask_path Please ask for path.
--help Show this message and exit.
```
#### scratch
Example of usage:
```bash
bu-isciii scratch --direction service_to_scratch <resolution_id>
```
Help:
```bash
Usage: bu-isciii scratch [OPTIONS] <resolution id>
Copy service folder to scratch directory for execution.
Options:
-p, --path PATH Absolute path to the folder containing
service to copy
-a, --ask_path Please ask for service path.
-t, --tmp_dir PATH Directory to which the files will be
transfered for execution. Default:
/data/bi/scratch_tmp/bi/
-d, --direction [service_to_scratch|scratch_to_service|remove_scratch]
Direction of the rsync command.
service_to_scratch from /data/bi/service to
/data/bi/scratch_tmp/bi/.scratch_to_service:
From /data/bi/scratch_tmp/bi/ to
/data/bi/service
--help Show this message and exit.
```
#### Finish
Example of usage:
```bash
bu-isciii finish <resolution_id>
```
Help:
```bash
Usage: bu-isciii finish [OPTIONS] <resolution id>
Service cleaning, remove big files, rename folders before copy and copy
resolution FOLDER to sftp.
Options:
-p, --path PATH Absolute path to the folder containg the service to
reaname and copy
-a, --ask_path Please ask for path, not assume pwd.
-s, --sftp_folder PATH Absolute path to directory to which the files will
be transfered
-t, --tmp_dir PATH Absolute path to the scratch directory containing
the service.
--help Show this message and exit.
```
Finish module performs de following modules at onin this order, at once:
##### clean
Example of usage:
```bash
bu-isciii clean <resolution_id>
```
Help:
```bash
Usage: bu-isciii clean [OPTIONS] <resolution id>
Service cleaning. It will either remove big files, rename folders before
copy, revert this renaming, show removable files or show folders for no
copy.
Options:
-p, --path PATH Absolute path to the folder containing
service to clean
-a, --ask_path Please ask for path
-s, --option [full_clean|rename_nocopy|clean|revert_renaming|show_removable|show_nocopy]
Select what to do inside the cleanning step:
full_clean: delete files and folders to
clean, rename no copy and deleted folders,
rename_nocopy: just rename no copy folders,
clean: delete files and folders to
clean,revert_renaming: remove no_copy and
delete tags,show_removable: list folders and
files to remove and show_nocopy: show
folders to rename with no_copy tag.
--help Show this message and exit.
```
##### scratch back
```bash
bu-isciii scratch --direction scratch_to_service <resolution_id>
```
##### copy_sftp
Example of usage:
```bash
bu-isciii copy-sftp <resolution_id>
```
Help:
```bash
Usage: bu-isciii copy-sftp [OPTIONS] <resolution id>
Copy resolution FOLDER to sftp, change status of resolution in iskylims and
generate md, pdf, html.
Options:
-p, --path PATH Absolute path to directory containing files to
transfer
-a, --ask_path Please ask for path
-s, --sftp_folder PATH Absolute path to directory to which the files will
be transfered
--help Show this message and exit.
```
#### bioinfo_doc
Example of usage:
```bash
bu-isciii bioinfo-doc <resolution_id>
```
Help:
```bash
Usage: bu-isciii bioinfo-doc [OPTIONS] <resolution id>
Create the folder documentation structure in bioinfo_doc server
Options:
-p, --path PATH Absolute path to bioinfo_doc directory.
-a, --ask_path Please ask for path, not assume
/data/bioinfo_doc/.
-t, --type [service_info|delivery]
Select the documentation that will generate
-s, --sftp_folder PATH Absolute path to sftp folfer containing
service folder
-r, --report_md PATH Absolute path to markdown report to use
instead of the one in config file
-m, --results_md PATH Absolute path to markdown report to use
instead of the one in config file
-e, --email_psswd TEXT Password for bioinformatica@isciii.es
--help Show this message and exit.
```
#### archive
Example of usage:
```bash
bu-isciii archive --date_from 2022-01-01 --date_until 2023-01-01
```
Help:
```bash
Usage: bu-isciii archive [OPTIONS]
Archive services or retrieve services from archive
Options:
-s, --service_id TEXT service id, pe SRVCNM787
-sf, --service_file TEXT file with services ids, one per line
-t, --ser_type [services_and_colaborations|research]
Select which folder you want to archive.
-o, --option [archive|retrieve_from_archive]
Select either you want to archive services
or retrieve a service from archive.
-sp, --skip_prompts Avoid prompts (except on service choosing)
-df, --date_from TEXT The date from which start search (format
'YYYY-MM-DD')
-du, --date_until TEXT The date from which end search (format
'YYYY-MM-DD')
-f, --output_name TEXT Tsv output path + filename with archive
stats and info
--help Show this message and exit.
```
#### autoclean_sftp
Example of usage:
```bash
bu-isciii autoclean-sftp
```
Help:
```bash
Usage: bu-isciii autoclean-sftp [OPTIONS]
Clean old sftp services
Options:
-s, --sftp_folder PATH Absolute path to sftp folder
-d, --days INTEGER Integer, remove files older than a window of `-d
[int]` days. Default 14 days.
--help Show this message and exit.
```
#### fix-permissions
Example of usage:
```bash
bu-isciii fix-permissions -d /data/bi
```
Help:
```bash
Usage: bu-isciii fix-permissions [OPTIONS]
Fix permissions
Options:
-d, --input_directory PATH Input directory to fix permissions (absolute path) [required]
--help Show this message and exit.
```
## Acknowledgements
Python package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools).
Raw data
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"maintainer_email": null,
"keywords": "buisciii, bioinformatics, pipeline, sequencing, NGS, next generation sequencing",
"author": "Sara Monzon",
"author_email": "smonzon@isciii.es",
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"description": "# buisciii-tools\n\n[](https://github.com/BU-ISCIII/buisciii-tools/actions/workflows/python_lint.yml)\n[](https://github.com/psf/black)\n\nBU-ISCIII provides a serie or services in its portfolio for supporting bioinformatics analysis to the labs in the Institute of Health Carlos III. bu-isciii tools is a set of helper tools for management of these bioinformatics analysis together with the LIMS ([iSkyLIMS](https://github.com/BU-ISCIII/iSkyLIMS))\n\n- [buisciii-tools](#buisciii-tools)\n - [Installation](#installation)\n - [Micromamba and pip](#micromamba-and-pip)\n - [Dev version](#dev-version)\n - [Usage](#usage)\n - [Command-line](#command-line)\n - [list](#list)\n - [new-service](#new-service)\n - [scratch](#scratch)\n - [Finish](#finish)\n - [clean](#clean)\n - [scratch back](#scratch-back)\n - [copy\\_sftp](#copy_sftp)\n - [bioinfo\\_doc](#bioinfo_doc)\n - [archive](#archive)\n - [autoclean\\_sftp](#autoclean_sftp)\n - [fix-permissions](#fix-permissions)\n - [Acknowledgements](#acknowledgements)\n\n## Installation\n\n### Micromamba and pip\n\n```bash\nmicromamba create -n buisciii -f environment.yml\nmicromamba activate buisciii\npip install buisciii-tools\n```\n\nor\n\n```bash\ngit checkout main\nconda create -n buisciii -f environment.yml\nconda activate \npip install buisciii-tools\n```\n\n### Dev version\n\nIf you want to install the latest code in the repository:\n\n```bash\nmicromamba create -n buisciii_dev -f environment.yml\nmicromamba activate buisciii_dev\npip install --force-reinstall --upgrade git+https://github.com/bu-isciii/buisciii-tools.git@develop\n```\n\nor locally:\n\n```bash\ngit checkout develop\nmicromamba create -n buisciii_dev -f environment.yml\nmicromamba activate buisciii_dev\npip install .\n```\n\n## Usage\n\n### Command-line\n\nRun bu-isciii tools:\n\n```bash\nbu-isciii --help\n```\n\nOutputs the following:\n\n```bash\nUsage: bu-isciii [OPTIONS] COMMAND [ARGS]...\n\nOptions:\n --version Show the version and exit.\n -v, --verbose Print verbose output to the console.\n -l, --log-file <filename> Save a verbose log to a file.\n -u, --api_user TEXT User for the API logging\n -p, --api_password TEXT Password for the API logging\n -c, --cred_file TEXT Config file with API logging credentials\n --help Show this message and exit\n\nCommands:\n list List available bu-isciii services.\n clean Service cleaning.\n new-service Create new service, it will create folder and copy...\n scratch Copy service folder to scratch directory for execution.\n copy-sftp Copy resolution FOLDER to sftp, change status of...\n finish Service cleaning, remove big files, rename folders before...\n bioinfo-doc Create the folder documentation structure in bioinfo_doc...\n archive Archive services or retrieve services from archive\n autoclean-sftp Clean old sftp services\n fix-permissions Fix permissions\n```\n\n#### list\n\nList available bu-isciii services:\n\n```bash\nbu-isciii list\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii list [OPTIONS] <service>\n\n List available bu-isciii services.\n\nOptions:\n --help Show this message and exit.\n```\n\nOutput:\n\n```bash\n\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2533\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2513\n\u2503 Service name \u2503 Description \u2503 Github \u2503\n\u2521\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2547\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2529\n\u2502 assembly_annotation \u2502 Nextflow assembly pipeline to assemble \u2502 https://github.com/Daniel-VM/bacass/... \u2502\n\u2502 \u2502 bacterial genomes \u2502 \u2502\n\u2502 mtbseq_assembly \u2502 Mycobacterium tuberculosis mapping, \u2502 https://github.com/ngs-fzb/MTBseq_source \u2502\n\u2502 \u2502 variant calling and detection of \u2502 \u2502\n\u2502 \u2502 resistance using MTBseq \u2502 \u2502\n\u2502 mtbseq \u2502 Mycobacterium tuberculosis mapping, \u2502 https://github.com/ngs-fzb/MTBseq_source \u2502\n\u2502 \u2502 variant calling and detection of \u2502 \u2502\n\u2502 \u2502 resistance using MTBseq \u2502 \u2502\n\u2502 pikavirus \u2502 PikaVirus, a mapping-based tool for \u2502 https://github.com/BU-ISCIII/PikaVirus \u2502\n\u2502 \u2502 metagenome analysis of virus. \u2502 \u2502\n\u2502 plasmidid_assembly \u2502 Plasmid identification tool based on \u2502 https://github.com/BU-ISCIII/plasmidID \u2502\n\u2502 \u2502 mapping and assisted by assembly \u2502 \u2502\n\u2502 wgmlst_taranis \u2502 Multilocus sequence typing (MLST) using \u2502 https://github.com/BU-ISCIII/taranis \u2502\n\u2502 \u2502 Taranis \u2502 \u2502\n\u2502 wgmlst_chewbbaca \u2502 Multilocus sequence typing (MLST) using \u2502 https://github.com/B-UMMI/chewBBACA \u2502\n\u2502 \u2502 chewBBACA \u2502 \u2502\n\u2502 viralrecon \u2502 Viral genome reconstruction analysis for \u2502 https://github.com/BU-ISCIII/viralrecon \u2502\n\u2502 \u2502 SARS-COV-2 data \u2502 \u2502\n\u2502 rnaseq \u2502 RNA-seq analysis \u2502 https://github.com/nf-core/rnaseq \u2502\n\u2502 lowfreq_panel \u2502 Low frequency variant calling from \u2502 \u2502\n\u2502 \u2502 enrichment panel. \u2502 \u2502\n\u2502 snippy \u2502 Rapid haploid variant calling and core \u2502 https://github.com/tseemann/snippy \u2502\n\u2502 \u2502 genome alignment \u2502 \u2502\n\u2502 seek_and_destroy \u2502 Simple pipeline for basic quality \u2502 https://github.com/GuilleGorines/Seek-Des\u2026 \u2502\n\u2502 \u2502 control, host removal and exploratory \u2502 \u2502\n\u2502 \u2502 analysis of samples. \u2502 \u2502\n\u2502 ariba_characterization \u2502 \u2502 \u2502\n\u2502 mag_met \u2502 1- Bioinformatics best-practise analysis \u2502 https://github.com/nf-core/mag or \u2502\n\u2502 \u2502 for taxonomic classification and \u2502 https://github.com/nf-core/taxprofiler \u2502\n\u2502 \u2502 profiling; 2- Bioinformatics best-practise\u2502 \u2502\n\u2502 \u2502 analysis pipeline for assembly, binning \u2502 \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2534\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\n```\n\n#### new-service\n\nExample of usage:\n\n```bash\nbu-isciii new-service <resolution_id>\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii new-service [OPTIONS] <resolution id>\n\n Create new service, it will create folder and copy template depending on\n selected service.\n\nOptions:\n -p, --path PATH Path to create the service folder\n -n, --no_create_folder No create service folder, only resolution\n -a, --ask_path Please ask for path.\n --help Show this message and exit.\n```\n\n#### scratch\n\nExample of usage:\n\n```bash\nbu-isciii scratch --direction service_to_scratch <resolution_id>\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii scratch [OPTIONS] <resolution id>\n\n Copy service folder to scratch directory for execution.\n\nOptions:\n -p, --path PATH Absolute path to the folder containing\n service to copy\n -a, --ask_path Please ask for service path.\n -t, --tmp_dir PATH Directory to which the files will be\n transfered for execution. Default:\n /data/bi/scratch_tmp/bi/\n -d, --direction [service_to_scratch|scratch_to_service|remove_scratch]\n Direction of the rsync command.\n service_to_scratch from /data/bi/service to\n /data/bi/scratch_tmp/bi/.scratch_to_service:\n From /data/bi/scratch_tmp/bi/ to\n /data/bi/service\n --help Show this message and exit.\n```\n\n#### Finish\n\nExample of usage:\n\n```bash\nbu-isciii finish <resolution_id>\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii finish [OPTIONS] <resolution id>\n\n Service cleaning, remove big files, rename folders before copy and copy\n resolution FOLDER to sftp.\n\nOptions:\n -p, --path PATH Absolute path to the folder containg the service to\n reaname and copy\n -a, --ask_path Please ask for path, not assume pwd.\n -s, --sftp_folder PATH Absolute path to directory to which the files will\n be transfered\n -t, --tmp_dir PATH Absolute path to the scratch directory containing\n the service.\n --help Show this message and exit.\n```\n\nFinish module performs de following modules at onin this order, at once:\n\n##### clean\n\nExample of usage:\n\n```bash\nbu-isciii clean <resolution_id>\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii clean [OPTIONS] <resolution id>\n\n Service cleaning. It will either remove big files, rename folders before\n copy, revert this renaming, show removable files or show folders for no\n copy.\n\nOptions:\n -p, --path PATH Absolute path to the folder containing\n service to clean\n -a, --ask_path Please ask for path\n -s, --option [full_clean|rename_nocopy|clean|revert_renaming|show_removable|show_nocopy]\n Select what to do inside the cleanning step:\n full_clean: delete files and folders to\n clean, rename no copy and deleted folders,\n rename_nocopy: just rename no copy folders,\n clean: delete files and folders to\n clean,revert_renaming: remove no_copy and\n delete tags,show_removable: list folders and\n files to remove and show_nocopy: show\n folders to rename with no_copy tag.\n --help Show this message and exit.\n```\n\n##### scratch back\n\n```bash\nbu-isciii scratch --direction scratch_to_service <resolution_id>\n```\n\n##### copy_sftp\n\nExample of usage:\n\n```bash\nbu-isciii copy-sftp <resolution_id>\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii copy-sftp [OPTIONS] <resolution id>\n\n Copy resolution FOLDER to sftp, change status of resolution in iskylims and\n generate md, pdf, html.\n\nOptions:\n -p, --path PATH Absolute path to directory containing files to\n transfer\n -a, --ask_path Please ask for path\n -s, --sftp_folder PATH Absolute path to directory to which the files will\n be transfered\n --help Show this message and exit.\n```\n\n#### bioinfo_doc\n\nExample of usage:\n\n```bash\nbu-isciii bioinfo-doc <resolution_id>\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii bioinfo-doc [OPTIONS] <resolution id>\n\n Create the folder documentation structure in bioinfo_doc server\n\nOptions:\n -p, --path PATH Absolute path to bioinfo_doc directory.\n -a, --ask_path Please ask for path, not assume\n /data/bioinfo_doc/.\n -t, --type [service_info|delivery]\n Select the documentation that will generate\n -s, --sftp_folder PATH Absolute path to sftp folfer containing\n service folder\n -r, --report_md PATH Absolute path to markdown report to use\n instead of the one in config file\n -m, --results_md PATH Absolute path to markdown report to use\n instead of the one in config file\n -e, --email_psswd TEXT Password for bioinformatica@isciii.es\n --help Show this message and exit.\n```\n\n#### archive\n\nExample of usage:\n\n```bash\nbu-isciii archive --date_from 2022-01-01 --date_until 2023-01-01\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii archive [OPTIONS]\n\n Archive services or retrieve services from archive\n\nOptions:\n -s, --service_id TEXT service id, pe SRVCNM787\n -sf, --service_file TEXT file with services ids, one per line\n -t, --ser_type [services_and_colaborations|research]\n Select which folder you want to archive.\n -o, --option [archive|retrieve_from_archive]\n Select either you want to archive services\n or retrieve a service from archive.\n -sp, --skip_prompts Avoid prompts (except on service choosing)\n -df, --date_from TEXT The date from which start search (format\n 'YYYY-MM-DD')\n -du, --date_until TEXT The date from which end search (format\n 'YYYY-MM-DD')\n -f, --output_name TEXT Tsv output path + filename with archive\n stats and info\n --help Show this message and exit.\n```\n\n#### autoclean_sftp\n\nExample of usage:\n\n```bash\nbu-isciii autoclean-sftp\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii autoclean-sftp [OPTIONS]\n\n Clean old sftp services\n\nOptions:\n -s, --sftp_folder PATH Absolute path to sftp folder\n -d, --days INTEGER Integer, remove files older than a window of `-d\n [int]` days. Default 14 days.\n --help Show this message and exit.\n```\n\n#### fix-permissions\n\nExample of usage:\n\n```bash\nbu-isciii fix-permissions -d /data/bi\n```\n\nHelp:\n\n```bash\nUsage: bu-isciii fix-permissions [OPTIONS]\n\n Fix permissions\n\nOptions:\n -d, --input_directory PATH Input directory to fix permissions (absolute path) [required]\n --help Show this message and exit.\n```\n\n## Acknowledgements\n\nPython package idea and design is really inspired in [nf-core/tools](https://github.com/nf-core/tools).\n",
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