scRNA template

inst/extdata/workflows/SPscrna/.batchtools.conf.R

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+cluster.functions <- makeClusterFunctionsSlurm(template="batchtools.slurm.tmpl")                      
+

inst/extdata/workflows/SPscrna/SPscrna.Rmd

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+---
+title: "Single Cell RNAseq" 
+author: "Author: FirstName LastName"
+date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" 
+output:
+  BiocStyle::html_document:
+    toc_float: true
+    code_folding: show
+  BiocStyle::pdf_document: default
+package: systemPipeR
+vignette: |
+  %\VignetteIndexEntry{RIBO-Seq Workflow Template}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+fontsize: 14pt
+bibliography: bibtex.bib
+editor_options: 
+  chunk_output_type: console
+---
+
+<!--
+Config css and r style
+-->
+
+```{css, echo=FALSE}
+pre code {
+white-space: pre !important;
+overflow-x: scroll !important;
+word-break: keep-all !important;
+word-wrap: initial !important;
+}
+```
+
+```{r style, echo = FALSE, results = 'asis'}
+BiocStyle::markdown()
+options(width=60, max.print=1000)
+knitr::opts_chunk$set(
+    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
+    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), 
+    tidy.opts=list(width.cutoff=60), tidy=TRUE)
+```
+
+```{r setup, echo=FALSE, message=FALSE, warning=FALSE, eval=FALSE}
+suppressPackageStartupMessages({
+    library(systemPipeR)
+})
+```
+
+# About the template
+This section provides general description and how to use this single cell RNAseq (scRNAseq) workflow. 
+In the actual analysis report, this  section is usually **removed**. 
+
+This scRNAseq workflow template is based on the 
+
+
+This workflow does:
+1. 
+
+
+![](results/plotwf_spscrna.jpg)
+
+# Introduction
+
+Users want to provide here background information about the design of their
+scRNAseq project.
+
+This report describes the analysis of a scRNAseq project studying drug ...
+
+## Experimental design
+
+Typically, users want to specify here all information relevant for the
+analysis of their scRNAseq study. This includes detailed descriptions of
+files, experimental design, reference genome, gene annotations,
+etc.
+
+# Workflow environment
+
+_`systemPipeR`_ workflows can be designed and built from start to finish with a 
+single command, importing from an R Markdown file or stepwise in interactive 
+mode from the R console. 
+
+This tutorial will demonstrate how to build the workflow in an interactive mode, 
+appending each step. The workflow is constructed by connecting each step via 
+`appendStep` method. Each `SYSargsList` instance contains instructions needed 
+for processing a set of input files with a specific command-line or R software 
+and the paths to the corresponding outfiles generated by a particular tool/step. 
+
+To create a Workflow within _`systemPipeR`_, we can start by defining an empty
+container and checking the directory structure:
+
+```{r create_workflow, message=FALSE, eval=FALSE}
+library(systemPipeR)
+sal <- SPRproject()
+sal
+```
+
+## Load packages 
+
+This is an empty template that contains only one demo step. 
+Refer to our [website](https://systempipe.org/sp/spr/spr_run/) for how to 
+add more steps. If you prefer a more enriched template, 
+[read this page](https://systempipe.org/sp/spr/templates/) for other 
+pre-configured templates.
+
+```{r load_packages, eval=FALSE, spr=TRUE}
+cat(crayon::blue$bold("To use this workflow, following R packages are expected:\n"))
+cat(c("'Seurat", "readr'\n"), sep = "', '")
+###pre-end
+appendStep(sal) <- LineWise(
+    code = {
+        library(systemPipeR)
+        library(rBLAST)
+    }, 
+    step_name = "load_packages"
+)
+```
+
+
+## Workflow session
+
+```{r wf_session, eval=FALSE, spr=TRUE}
+appendStep(sal) <- LineWise(
+    code = {
+        sessionInfo()
+    }, 
+    step_name = "wf_session", 
+    dependency = "xxx")
+```
+
+# Manage the workflow
+
+To run the workflow, use `runWF` function. It executes all the steps store in 
+the workflow container. The execution will be on a single machine without 
+submitting to a queuing system of a computer cluster. 
+
+```{r runWF, eval=FALSE}
+sal <- runWF(sal, run_step = "mandatory") # remove `run_step` to run all steps to include optional steps
+```
+
+- To use complex workflow control options, such as parallelization, subsetting samples, selecting steps, read the [documents](https://systempipe.org/sp/spr/sp_run/step_run/) on our website. 
+- Explore [other details of the workflow object](https://systempipe.org/sp/spr/sp_run/sal_explore/).
+- Create [logs and reports](https://systempipe.org/sp/spr/sp_run/step_reports/).
+- [Visualize the workflow](https://systempipe.org/sp/spr/sp_run/step_vis/).
+
+# About the workflow
+## Tools used 
+To check command-line tools used in this workflow, use `listCmdTools`, and use `listCmdModules`
+to check if you have a modular system.
+
+The following code will print out tools required in your custom SPR project in the report. 
+In case you are running the workflow for the first and do not have a project yet, or you 
+just want to browser this workflow, following code displays the tools required by default.
+```{r list_tools}
+if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
+    local({
+        sal <- systemPipeR::SPRproject(resume = TRUE)
+        systemPipeR::listCmdTools(sal)
+        systemPipeR::listCmdModules(sal)
+    })
+} else {
+    cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
+    cat(c("NA"), sep = "\n")
+}
+```
+
+
+## Session Info
+This is the session information for rendering this report. To access the session information
+of workflow running, check HTML report of `renderLogs`. 
+```{r report_session_info, eval=TRUE}
+sessionInfo()
+```

inst/extdata/workflows/SPscrna/batchtools.slurm.tmpl

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+#!/bin/bash
+
+## Job Resource Interface Definition
+##
+## ntasks [integer(1)]:       Number of required tasks,
+##                            Set larger than 1 if you want to further parallelize
+##                            with MPI within your job.
+## ncpus [integer(1)]:        Number of required cpus per task,
+##                            Set larger than 1 if you want to further parallelize
+##                            with multicore/parallel within each task.
+## walltime [integer(1)]:     Walltime for this job, in minutes.
+##                            Must be at least 1 minute.
+## memory   [integer(1)]:     Memory in megabytes for each cpu.
+##                            Must be at least 100 (when I tried lower values my
+##                            jobs did not start at all).
+##
+## Default resources can be set in your .batchtools.conf.R by defining the variable
+## 'default.resources' as a named list.
+
+<%
+# relative paths are not handled well by Slurm
+log.file = normalizePath(log.file, winslash = "/", mustWork = FALSE)
+-%>
+
+
+#SBATCH --job-name=<%= job.name %>
+#SBATCH --output=<%= log.file %>
+#SBATCH --error=<%= log.file %>
+#SBATCH --time=<%= ceiling(resources$walltime / 1) %>
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=<%= resources$ncpus %>
+#SBATCH --mem-per-cpu=<%= resources$memory %>
+<%= if (!is.null(resources$partition)) sprintf(paste0("#SBATCH --partition='", resources$partition, "'")) %>
+<%= if (array.jobs) sprintf("#SBATCH --array=1-%i", nrow(jobs)) else "" %>
+
+## specify which queue on biocluster, one of 'batch', 'highmem', 'intel', 'gpu', 'mygroup'
+#SBATCH -p short
+##SBATCH -p batch
+##SBATCH -p intel 
+
+## Initialize work environment like
+## source /etc/profile
+## module add ...
+
+## Export value of DEBUGME environemnt var to slave
+export DEBUGME=<%= Sys.getenv("DEBUGME") %>
+
+## Run R:
+## we merge R output with stdout from SLURM, which gets then logged via --output option
+Rscript -e 'batchtools::doJobCollection("<%= uri %>")'
+