A tool to fetch workflow and config files from a Snakemake repository on GitHub.
Although snakedeploy
can be used to prepare Snakemake
workflows, this does not always work.
snakefetch
is basically a simpler version of snakedeploy
that will copy the config and workflow directories of any Snakemake
workflow on github into any directory.
snakefetch
can be installed via pip:
$ pip install snakefetch
To update snakefetch
:
$ pip install snakefetch -U
$ snakefetch --help
usage: snakefetch [-h] [--outdir OUTDIR] --url URL --repo-version REPOVERSION [--target-dirs TARGETDIRS] [--version]
Fetch config and workflow directories from a versioned Snakemake repository on GitHub
options:
-h, --help show this help message and exit
--outdir OUTDIR, -o OUTDIR
Directory to save the files to
--url URL, -u URL URL of the Snakemake repository on GitHub
--repo-version REPOVERSION, -v REPOVERSION
Release version of the Snakemake repository on GitHub
--target-dirs TARGETDIRS, -t TARGETDIRS
Directories to fetch from the Snakemake repository on GitHub (default: config,workflow)
--version Print snakefetch version and exit
$ snakefetch --version
snakefetch version 0.5.2
$ snakefetch -o /home/niek/TEST -v v0.4.0 -u https://github.com/niekwit/damid-seq
Downloading archive file for version v0.4.0 from https://github.com/niekwit/damid-seq...
Extracting config and workflow directories from tar.gz file to /home/niek/Downloads/TEST...
Done!
$ cd /home/niek/TEST
$ tree
.
├── config
│ ├── config.yaml
│ ├── README.md
│ └── samples.csv
└── workflow
├── envs
│ ├── damid.yaml
│ ├── deeptools.yaml
│ ├── peak_calling.yaml
│ ├── R.yaml
│ └── trim.yaml
├── report
│ ├── annotated_peaks.rst
│ ├── correlation.rst
│ ├── distance_to_tss.rst
│ ├── feature_distributions.rst
│ ├── heatmap.rst
│ ├── mapping_rates.rst
│ ├── pca.rst
│ ├── profile_plot.rst
│ ├── scree.rst
│ └── workflow.rst
├── rules
│ ├── bedgraph_processing.smk
│ ├── bed.smk
│ ├── damid.smk
│ ├── deeptools.smk
│ ├── fastqc.smk
│ ├── motifs.smk
│ ├── peak_calling.smk
│ ├── plotting.smk
│ ├── resources.smk
│ └── trimming.smk
├── schemas
│ └── config.schema.yaml
├── scripts
│ ├── annotate_peaks.R
│ ├── average_bigwig.py
│ ├── average_wig.py
│ ├── bowtie2_align_to_plasmid.py
│ ├── convert_bed2fasta.py
│ ├── create_annotation_file.R
│ ├── create_background_fasta.py
│ ├── create_blacklist.py
│ ├── damidseq_pipeline.py
│ ├── filter_overlapping_peaks.py
│ ├── general_functions.smk
│ ├── get_resource.sh
│ ├── mask_fasta.py
│ ├── peak_annotation_plots.R
│ ├── plot_mapping_rates.R
│ ├── plot_PCA.R
│ ├── quantile_norm_bedgraph.py
│ ├── resources.py
│ ├── reverse_log2.py
│ ├── run_find_peaks.py
│ └── trim_galore.py
└── Snakefile
7 directories, 51 files