From 235f242e742952018c7530acb7b9e94dc31740ab Mon Sep 17 00:00:00 2001 From: skchronicles Date: Tue, 20 Jun 2023 16:58:38 -0400 Subject: [PATCH] Setting up chrom-seek pipeline --- .github/workflows/main.yaml | 2 +- CHANGELOG.md | 2 +- README.md | 34 +++++++++++------------ VERSION | 2 +- baseline => chrom-seek | 55 +++++++++++++++++++++++++++---------- docs/README.md | 6 ++-- docs/faq/questions.md | 2 +- docs/index.md | 42 ++++++++++++++-------------- docs/usage/cache.md | 16 +++++------ docs/usage/install.md | 24 ++++++++-------- docs/usage/run.md | 26 +++++++++--------- docs/usage/unlock.md | 14 +++++----- mkdocs.yml | 18 ++++++------ 13 files changed, 135 insertions(+), 108 deletions(-) rename baseline => chrom-seek (92%) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index ce3a292..72095ce 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -18,7 +18,7 @@ jobs: - name: Dry Run with test data run: | docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ - /opt2/baseline run --input \ + /opt2/chrom-seek run --input \ /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ /opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \ /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \ diff --git a/CHANGELOG.md b/CHANGELOG.md index 0b11cb7..6ec66c6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,6 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [0.1.0] - 2022-08-22 +## [0.1.0] - 2023-06-20 ### Added - Recommended [scaffold](https://github.com/OpenOmics/baseline) for building a snakemake pipeline diff --git a/README.md b/README.md index c4180b9..97c6c9c 100644 --- a/README.md +++ b/README.md @@ -1,33 +1,33 @@
-

baseline 🔬

+

chrom-seek 🔬

- **_long pipeline name_** + **_An awesome set of eipgenetic pipelines_** - [![tests](https://github.com/OpenOmics/baseline/workflows/tests/badge.svg)](https://github.com/OpenOmics/baseline/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/baseline/workflows/docs/badge.svg)](https://github.com/OpenOmics/baseline/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/baseline?color=brightgreen)](https://github.com/OpenOmics/baseline/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/baseline)](https://github.com/OpenOmics/baseline/blob/main/LICENSE) + [![tests](https://github.com/OpenOmics/chrom-seek/workflows/tests/badge.svg)](https://github.com/OpenOmics/chrom-seek/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/chrom-seek/workflows/docs/badge.svg)](https://github.com/OpenOmics/chrom-seek/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/chrom-seek?color=brightgreen)](https://github.com/OpenOmics/chrom-seek/issues) [![GitHub license](https://img.shields.io/github/license/OpenOmics/chrom-seek)](https://github.com/OpenOmics/chrom-seek/blob/main/LICENSE) - This is the home of the pipeline, baseline. Its long-term goals: to accurately ...insert goal, to infer ...insert goal, and to boldly ...insert goal like no pipeline before! + This is the home of the pipeline, chrom-seek. Its long-term goals: to accurately call and annotate peaks, to infer cell types in cell-free samples, and to boldly quantify diferential binding or accessibility like no pipeline before!
## Overview -Welcome to baseline! Before getting started, we highly recommend reading through [baseline's documentation](https://openomics.github.io/baseline/). +Welcome to chrom-seek! Before getting started, we highly recommend reading through [chrom-seek's documentation](https://openomics.github.io/chrom-seek/). -The **`./baseline`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions: +The **`./chrom-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions: - * [baseline run](https://openomics.github.io/baseline/usage/run/): Run the baseline pipeline with your input files. - * [baseline unlock](https://openomics.github.io/baseline/usage/unlock/): Unlocks a previous runs output directory. - * [baseline install](https://openomics.github.io/baseline/usage/install/): Download reference files locally. - * [baseline cache](https://openomics.github.io/baseline/usage/cache/): Cache remote resources locally, coming soon! + * [chrom-seek run](https://openomics.github.io/chrom-seek/usage/run/): Run the chrom-seek pipeline with your input files. + * [chrom-seek unlock](https://openomics.github.io/chrom-seek/usage/unlock/): Unlocks a previous runs output directory. + * [chrom-seek install](https://openomics.github.io/chrom-seek/usage/install/): Download reference files locally. + * [chrom-seek cache](https://openomics.github.io/chrom-seek/usage/cache/): Cache remote resources locally, coming soon! -**baseline** is a comprehensive ...insert long description. It relies on technologies like [Singularity1](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake2](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster. +**chrom-seek** is an an awesome set of pipelines designed specfically for cell-free ChIP-seq, bulk ChIP-seq, and bulk ATAC-seq sequencing data. It relies on technologies like [Singularity1](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake2](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster. The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users. -Before getting started, we highly recommend reading through the [usage](https://openomics.github.io/baseline/usage/run/) section of each available sub command. +Before getting started, we highly recommend reading through the [usage](https://openomics.github.io/chrom-seek/usage/run/) section of each available sub command. -For more information about issues or trouble-shooting a problem, please checkout our [FAQ](https://openomics.github.io/baseline/faq/questions/) prior to [opening an issue on Github](https://github.com/OpenOmics/baseline/issues). +For more information about issues or trouble-shooting a problem, please checkout our [FAQ](https://openomics.github.io/chrom-seek/faq/questions/) prior to [opening an issue on Github](https://github.com/OpenOmics/chrom-seek/issues). ## Dependencies **Requires:** `singularity>=3.5` `snakemake>=6.0` @@ -38,18 +38,18 @@ At the current moment, the pipeline uses a mixture of enviroment modules and doc Please clone this repository to your local filesystem using the following command: ```bash # Clone Repository from Github -git clone https://github.com/OpenOmics/baseline.git +git clone https://github.com/OpenOmics/chrom-seek.git # Change your working directory -cd baseline/ +cd chrom-seek/ # Add dependencies to $PATH # Biowulf users should run module load snakemake singularity # Get usage information -./baseline -h +./chrom-seek -h ``` ## Contribute -This site is a living document, created for and by members like you. baseline is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository](https://github.com/OpenOmics/baseline). +This site is a living document, created for and by members like you. chrom-seek is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository](https://github.com/OpenOmics/chrom-seek). ## Cite diff --git a/VERSION b/VERSION index 6e8bf73..a67658d 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.1.0 +0.1.0-beta diff --git a/baseline b/chrom-seek similarity index 92% rename from baseline rename to chrom-seek index bb3cd87..975d23f 100755 --- a/baseline +++ b/chrom-seek @@ -25,9 +25,9 @@ merchantability or fitness for any particular purpose. Please cite the author and NIH resources like the "Biowulf Cluster" in any work or product based on this material. USAGE: - $ baseline [OPTIONS] + $ chrom-seek [OPTIONS] EXAMPLE: - $ baseline run --input *.R?.fastq.gz --output output/ + $ chrom-seek run --input *.R?.fastq.gz --output output/ """ # Python standard library @@ -49,16 +49,17 @@ from src.utils import ( hashed, permissions, check_cache, - require) + require +) # Pipeline Metadata __version__ = version -__authors__ = 'Skyler Kuhn' -__email__ = 'skyler.kuhn@nih.gov' +__authors__ = 'Skyler Kuhn, Tovah Markowitz' +__email__ = 'skyler.kuhn@nih.gov, tovah.markowitz@nih.gov' __home__ = os.path.dirname(os.path.abspath(__file__)) _name = os.path.basename(sys.argv[0]) -_description = 'An awesome baseline pipeline' +_description = 'An awesome set of epigenetic pipelines' def unlock(sub_args): @@ -217,7 +218,7 @@ def parsed_arguments(name, description): """ # Add styled name and description c = Colors - styled_name = "{0}{1}{2}baseline{3}".format(c.bold, c.bg_black, c.cyan, c.end) + styled_name = "{0}{1}{2}chrom-seek{3}".format(c.bold, c.bg_black, c.cyan, c.end) description = "{0}{1}{2}".format(c.bold, description, c.end) # Create a top-level parser @@ -243,17 +244,39 @@ def parsed_arguments(name, description): [--dry-run] [--job-name JOB_NAME] [--mode {{slurm,local}}] \\ [--sif-cache SIF_CACHE] [--singularity-cache SINGULARITY_CACHE] \\ [--silent] [--threads THREADS] [--tmp-dir TMP_DIR] \\ + --assay {{cfChIP,ChIP,ATAC}} \\ + --genome GENOME \\ --input INPUT [INPUT ...] \\ - --output OUTPUT + --output OUTPUT Optional arguments are shown in square brackets above. {3}{4}Description:{5} - To run the ...long pipeline name with your data raw data, please - provide a space seperated list of FastQ (globbing is supported) and an output - directory to store results. + To run an available pipeline with your data raw data, please provide a space + seperated list of FastQ (globbing is supported), an output directory to store + results, a reference genome for alignment and annotation, and an assay type to + call a specific data-processing pipeline. {3}{4}Required arguments:{5} + --assay {{cfChIP,ChIP,ATAC}} + Assay type or data-processing pipeline. This option + defines which pipeline will be run. chrom-seek supports + the processing of bulk ChIP-seq (ChIP), cell-free DNA + ChIP-seq (cfChIP), and ATAC-seq (ATAC) samples. Select + from one of the following data-processing pipelines: + • ChIP + • cfChIP + • ATAC + Example: --assay ChIP + --genome GENOME + Reference genome. This option defines the reference + genome of the samples. modr does comes bundled with + prebuilt reference files from GENCODE for human and + mouse samples. Select one of the following options: + • hg19 + • hg38 + • mm10 + Example: --genome hg19 --input INPUT [INPUT ...] Input FastQ file(s) to process. The pipeline does NOT support single-end data. FastQ files for one or more @@ -356,7 +379,9 @@ def parsed_arguments(name, description): module load singularity snakemake # Step 2A.) Dry-run the pipeline - ./{0} run --input .tests/*.R?.fastq.gz \\ + ./{0} run --assay ChIP \\ + --genome hg19 \\ + --input .tests/*.R?.fastq.gz \\ --output /data/$USER/output \\ --mode slurm \\ --dry-run @@ -365,9 +390,11 @@ def parsed_arguments(name, description): # The slurm mode will submit jobs to # the cluster. It is recommended running # the pipeline in this mode. - ./{0} run --input .tests/*.R?.fastq.gz \\ + ./{0} run --assay ChIP \\ + --genome hg19 \\ + --input .tests/*.R?.fastq.gz \\ --output /data/$USER/output \\ - --mode slurm + --mode slurm {2}{3}Version:{4} {1} diff --git a/docs/README.md b/docs/README.md index 7e964c7..fa40932 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,12 +1,12 @@ # Build documentation -> **Please Note:** When a commit is pushed to the `docs/` directory, it triggers a [github actions workflow](https://github.com/OpenOmics/baseline/actions) to build the static-site and push it to the gh-pages branch. +> **Please Note:** When a commit is pushed to the `docs/` directory, it triggers a [github actions workflow](https://github.com/OpenOmics/chrom-seek/actions) to build the static-site and push it to the gh-pages branch. ### Installation ```bash # Clone the Repository -git clone https://github.com/OpenOmics/baseline.git -cd baseline/ +git clone https://github.com/OpenOmics/chrom-seek.git +cd chrom-seek/ # Create a virtual environment python3 -m venv .venv # Activate the virtual environment diff --git a/docs/faq/questions.md b/docs/faq/questions.md index 40c323d..6451f44 100644 --- a/docs/faq/questions.md +++ b/docs/faq/questions.md @@ -1,4 +1,4 @@ # Frequently Asked Questions -This page is still under construction. If you need immediate help, please [open an issue](https://github.com/OpenOmics/baseline/issues) on Github! +This page is still under construction. If you need immediate help, please [open an issue](https://github.com/OpenOmics/chrom-seek/issues) on Github! diff --git a/docs/index.md b/docs/index.md index 086219d..8f2b8c9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,43 +1,43 @@
-

baseline 🔬

+

chrom-seek 🔬

- long pipeline name
- - tests + An awesome set of eipgenetic pipelines
+ + tests - - docs + + docs - - GitHub issues + + GitHub issues - - GitHub license + + GitHub license

- This is the home of the pipeline, baseline. Its long-term goals: to accurately ...insert goal, to infer ...insert goal, and to boldly ...insert goal like no pipeline before! + This is the home of the pipeline, chrom-seek. Its long-term goals: to accurately call and annotate peaks, to infer cell types in cell-free samples, and to boldly quantify diferential binding or accessibility like no pipeline before!

## Overview -Welcome to baseline's documentation! This guide is the main source of documentation for users that are getting started with the [long pipeline name](https://github.com/OpenOmics/baseline/). +Welcome to chrom-seek's documentation! This guide is the main source of documentation for users that are getting started with the our [bulk epigenetic pipelines](https://github.com/OpenOmics/chrom-seek/). -The **`./baseline`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions: +The **`./chrom-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:
!!! inline custom-grid-button "" - [baseline run](usage/run.md) - Run the baseline pipeline with your input files. + [chrom-seek run](usage/run.md) + Run the chrom-seek pipeline with your input files. !!! inline custom-grid-button "" - [baseline unlock](usage/unlock.md) + [chrom-seek unlock](usage/unlock.md) Unlocks a previous runs output directory.
@@ -47,28 +47,28 @@ The **`./baseline`** pipeline is composed several inter-related sub commands to !!! inline custom-grid-button "" - [baseline install](usage/install.md) + [chrom-seek install](usage/install.md) Download remote reference files locally. !!! inline custom-grid-button "" - [baseline cache](usage/cache.md) + [chrom-seek cache](usage/cache.md) Cache remote software containers locally. -**baseline** is a comprehensive ...insert long description. It relies on technologies like [Singularity1](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake2](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster. +**chrom-seek** is an an awesome set of pipelines designed specfically for cell-free ChIP-seq, bulk ChIP-seq, and bulk ATAC-seq sequencing data. It relies on technologies like [Singularity1](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake2](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster. The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users. Before getting started, we highly recommend reading through the [usage](usage/run.md) section of each available sub command. -For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/OpenOmics/baseline/issues). +For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/OpenOmics/chrom-seek/issues). ## Contribute -This site is a living document, created for and by members like you. baseline is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/OpenOmics/baseline). +This site is a living document, created for and by members like you. chrom-seek is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/OpenOmics/chrom-seek). ## Citation diff --git a/docs/usage/cache.md b/docs/usage/cache.md index 82c433f..4c4f1f3 100644 --- a/docs/usage/cache.md +++ b/docs/usage/cache.md @@ -1,9 +1,9 @@ -# baseline cache +# chrom-seek cache ## 1. About -The `baseline` executable is composed of several inter-related sub commands. Please see `baseline -h` for all available options. +The `chrom-seek` executable is composed of several inter-related sub commands. Please see `chrom-seek -h` for all available options. -This part of the documentation describes options and concepts for baseline cache sub command in more detail. With minimal configuration, the **`cache`** sub command enables you to cache remote resources for the baseline pipeline. Caching remote resources allows the pipeline to run in an offline mode. The cache sub command can also be used to pull our pre-built reference bundles onto a new cluster or target system. +This part of the documentation describes options and concepts for chrom-seek cache sub command in more detail. With minimal configuration, the **`cache`** sub command enables you to cache remote resources for the chrom-seek pipeline. Caching remote resources allows the pipeline to run in an offline mode. The cache sub command can also be used to pull our pre-built reference bundles onto a new cluster or target system. The cache sub command creates local cache on the filesysytem for resources hosted on DockerHub or AWS S3. These resources are normally pulled onto the filesystem when the pipeline runs; however, due to network issues or DockerHub pull rate limits, it may make sense to pull the resources once so a shared cache can be created and re-used. It is worth noting that a singularity cache cannot normally be shared across users. Singularity strictly enforces that its cache is owned by the user. To get around this issue, the cache subcommand can be used to create local SIFs on the filesystem from images on DockerHub. @@ -12,14 +12,14 @@ The cache sub command creates local cache on the filesysytem for resources hoste Coming Soon! \ No newline at end of file diff --git a/docs/usage/install.md b/docs/usage/install.md index 548df6d..496996a 100644 --- a/docs/usage/install.md +++ b/docs/usage/install.md @@ -1,17 +1,17 @@ -# baseline install +# chrom-seek install ## 1. About -The `baseline` executable is composed of several inter-related sub commands. Please see `baseline -h` for all available options. +The `chrom-seek` executable is composed of several inter-related sub commands. Please see `chrom-seek -h` for all available options. -This part of the documentation describes options and concepts for baseline install sub command in more detail. +This part of the documentation describes options and concepts for chrom-seek install sub command in more detail. This page is still under construction 👷, more information is coming soon! \ No newline at end of file diff --git a/docs/usage/run.md b/docs/usage/run.md index 633b792..f7c7513 100644 --- a/docs/usage/run.md +++ b/docs/usage/run.md @@ -1,15 +1,15 @@ -# baseline run +# chrom-seek run ## 1. About -The `baseline` executable is composed of several inter-related sub commands. Please see `baseline -h` for all available options. +The `chrom-seek` executable is composed of several inter-related sub commands. Please see `chrom-seek -h` for all available options. -This part of the documentation describes options and concepts for baseline run sub command in more detail. With minimal configuration, the **`run`** sub command enables you to start running baseline pipeline. +This part of the documentation describes options and concepts for chrom-seek run sub command in more detail. With minimal configuration, the **`run`** sub command enables you to start running chrom-seek pipeline. -Setting up the baseline pipeline is fast and easy! In its most basic form, baseline run only has *two required inputs*. +Setting up the chrom-seek pipeline is fast and easy! In its most basic form, chrom-seek run only has *two required inputs*. ## 2. Synopsis ```text -$ baseline run [--help] \ +$ chrom-seek run [--help] \ [--mode {slurm,local}] [--job-name JOB_NAME] [--batch-id BATCH_ID] \ [--tmp-dir TMP_DIR] [--silent] [--sif-cache SIF_CACHE] \ [--singularity-cache SINGULARITY_CACHE] \ @@ -43,7 +43,7 @@ Each of the following arguments are required. Failure to provide a required argu > > This location is where the pipeline will create all of its output files, also known as the pipeline's working directory. If the provided output directory does not exist, it will be created automatically. > -> ***Example:*** `--output /data/$USER/baseline_out` +> ***Example:*** `--output /data/$USER/chrom-seek_out` ### 2.2 Analysis options @@ -81,7 +81,7 @@ Each of the following arguments are optional, and do not need to be provided. > Execution Method. Defines the mode or method of execution. Vaild mode options include: slurm or local. > > ***slurm*** -> The slurm execution method will submit jobs to the [SLURM workload manager](https://slurm.schedmd.com/). It is recommended running baseline in this mode as execution will be significantly faster in a distributed environment. This is the default mode of execution. +> The slurm execution method will submit jobs to the [SLURM workload manager](https://slurm.schedmd.com/). It is recommended running chrom-seek in this mode as execution will be significantly faster in a distributed environment. This is the default mode of execution. > > ***local*** > Local executions will run serially on compute instance. This is useful for testing, debugging, or when a users does not have access to a high performance computing environment. If this option is not provided, it will default to a local execution mode. @@ -92,9 +92,9 @@ Each of the following arguments are optional, and do not need to be provided. `--job-name JOB_NAME` > **Set the name of the pipeline's master job.** > *type: string* -> *default: pl:baseline* +> *default: pl:chrom-seek* > -> When submitting the pipeline to a job scheduler, like SLURM, this option always you to set the name of the pipeline's master job. By default, the name of the pipeline's master job is set to "pl:baseline". +> When submitting the pipeline to a job scheduler, like SLURM, this option always you to set the name of the pipeline's master job. By default, the name of the pipeline's master job is set to "pl:chrom-seek". > > ***Example:*** `--job-name pl_id-42` @@ -113,7 +113,7 @@ Each of the following arguments are optional, and do not need to be provided. > **Path where a local cache of SIFs are stored.** > *type: path* > -> Uses a local cache of SIFs on the filesystem. This SIF cache can be shared across users if permissions are set correctly. If a SIF does not exist in the SIF cache, the image will be pulled from Dockerhub and a warning message will be displayed. The `baseline cache` subcommand can be used to create a local SIF cache. Please see `baseline cache` for more information. This command is extremely useful for avoiding DockerHub pull rate limits. It also remove any potential errors that could occur due to network issues or DockerHub being temporarily unavailable. We recommend running baseline with this option when ever possible. +> Uses a local cache of SIFs on the filesystem. This SIF cache can be shared across users if permissions are set correctly. If a SIF does not exist in the SIF cache, the image will be pulled from Dockerhub and a warning message will be displayed. The `chrom-seek cache` subcommand can be used to create a local SIF cache. Please see `chrom-seek cache` for more information. This command is extremely useful for avoiding DockerHub pull rate limits. It also remove any potential errors that could occur due to network issues or DockerHub being temporarily unavailable. We recommend running chrom-seek with this option when ever possible. > > ***Example:*** `--singularity-cache /data/$USER/SIFs` @@ -158,16 +158,16 @@ module purge module load singularity snakemake # Step 2A.) Dry-run the pipeline -./baseline run --input .tests/*.R?.fastq.gz \ +./chrom-seek run --input .tests/*.R?.fastq.gz \ --output /data/$USER/output \ --mode slurm \ --dry-run -# Step 2B.) Run the baseline pipeline +# Step 2B.) Run the chrom-seek pipeline # The slurm mode will submit jobs to # the cluster. It is recommended running # the pipeline in this mode. -./baseline run --input .tests/*.R?.fastq.gz \ +./chrom-seek run --input .tests/*.R?.fastq.gz \ --output /data/$USER/output \ --mode slurm ``` \ No newline at end of file diff --git a/docs/usage/unlock.md b/docs/usage/unlock.md index 5a77d1b..37e4d51 100644 --- a/docs/usage/unlock.md +++ b/docs/usage/unlock.md @@ -1,19 +1,19 @@ -# baseline unlock +# chrom-seek unlock ## 1. About -The `baseline` executable is composed of several inter-related sub commands. Please see `baseline -h` for all available options. +The `chrom-seek` executable is composed of several inter-related sub commands. Please see `chrom-seek -h` for all available options. -This part of the documentation describes options and concepts for baseline unlock sub command in more detail. With minimal configuration, the **`unlock`** sub command enables you to unlock a pipeline output directory. +This part of the documentation describes options and concepts for chrom-seek unlock sub command in more detail. With minimal configuration, the **`unlock`** sub command enables you to unlock a pipeline output directory. If the pipeline fails ungracefully, it maybe required to unlock the working directory before proceeding again. Snakemake will inform a user when it maybe necessary to unlock a working directory with an error message stating: `Error: Directory cannot be locked`. Please verify that the pipeline is not running before running this command. If the pipeline is currently running, the workflow manager will report the working directory is locked. The is the default behavior of snakemake, and it is normal. Do NOT run this command if the pipeline is still running! Please kill the master job and it's child jobs prior to running this command. -Unlocking baseline pipeline output directory is fast and easy! In its most basic form, baseline unlock only has *one required input*. +Unlocking chrom-seek pipeline output directory is fast and easy! In its most basic form, chrom-seek unlock only has *one required input*. ## 2. Synopsis ```text -$ ./baseline unlock [-h] --output OUTPUT +$ ./chrom-seek unlock [-h] --output OUTPUT ``` The synopsis for this command shows its parameters and their usage. Optional parameters are shown in square brackets. @@ -29,7 +29,7 @@ Use you can always use the `-h` option for information on a specific command. > *type: path* > > Path to a previous run's output directory. This will remove a lock on the working directory. Please verify that the pipeline is not running before running this command. -> ***Example:*** `--output /data/$USER/baseline_out` +> ***Example:*** `--output /data/$USER/chrom-seek_out` ### 2.2 Options @@ -52,5 +52,5 @@ module purge module load singularity snakemake # Step 1.) Unlock a pipeline output directory -baseline unlock --output /data/$USER/output +chrom-seek unlock --output /data/$USER/output ``` \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index fa2c47d..e123f85 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,13 +1,13 @@ # Project Information -site_name: baseline +site_name: chrom-seek site_author: Skyler Kuhn site_description: >- - An awesome OpenOmics baseline pipeline + An awesome OpenOmics chrom-seek pipeline # Repository -repo_name: OpenOmics/baseline -repo_url: https://github.com/OpenOmics/baseline -edit_uri: https://github.com/OpenOmics/baseline/edit/main/docs/ +repo_name: OpenOmics/chrom-seek +repo_url: https://github.com/OpenOmics/chrom-seek +edit_uri: https://github.com/OpenOmics/chrom-seek/edit/main/docs/ # Extra extra_css: @@ -98,10 +98,10 @@ markdown_extensions: nav: - About: index.md - Commands: - - baseline run: usage/run.md - - baseline unlock: usage/unlock.md - - baseline install: usage/install.md - - baseline cache: usage/cache.md + - chrom-seek run: usage/run.md + - chrom-seek unlock: usage/unlock.md + - chrom-seek install: usage/install.md + - chrom-seek cache: usage/cache.md - FAQ: - General Questions: faq/questions.md - License: license.md