Merge pull request #77 from jfy133/documentation_improvements

Documentation improvements

Author: apeltzer

README.md

@@ -45,4 +45,4 @@ The nf-core/eager pipeline comes with documentation about the pipeline, found in
 5. [Troubleshooting](docs/troubleshooting.md)
 
 ### Credits
-This pipeline was written by Alexander Peltzer ([apeltzer](https://github.com/apeltzer)), with major contributions from Stephen Clayton, ideas and documentation from James Fellows-Yates, Raphael Eisenhofer and Judith Neukamm. If you want to contribute, please open an issue and ask to be added to the project - happy to do so and everyone is welcome to contribute here!
+This pipeline was written by Alexander Peltzer ([apeltzer](https://github.com/apeltzer)), with major contributions from Stephen Clayton, ideas and documentation from James Fellows Yates, Raphael Eisenhofer and Judith Neukamm. If you want to contribute, please open an issue and ask to be added to the project - happy to do so and everyone is welcome to contribute here!

docs/configuration/adding_your_own.md

@@ -51,7 +51,6 @@ Note that the dockerhub organisation name annoyingly can't have a hyphen, so is
 ### Singularity image
 Many HPC environments are not able to run Docker due to security issues.
 [Singularity](http://singularity.lbl.gov/) is a tool designed to run on such HPC systems which is very similar to Docker.
->>>>>>> TEMPLATE
 
 To specify singularity usage in your pipeline config file, add the following:
 
@@ -81,5 +80,4 @@ To use conda in your own config file, add the following:
 
 ```nextflow
 process.conda = "$baseDir/environment.yml"
->>>>>>> TEMPLATE
 ```

docs/installation.md

@@ -69,6 +69,19 @@ Be warned of two important points about this default configuration:
     * See the [nextflow docs](https://www.nextflow.io/docs/latest/executor.html) for information about running with other hardware backends. Most job scheduler systems are natively supported.
 2. Nextflow will expect all software to be installed and available on the `PATH`
 
+The following software is currently required to be installed:
+
+* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+* [Picard Tools](https://broadinstitute.github.io/picard/)
+* [Samtools](http://www.htslib.org/)
+* [Preseq](http://smithlabresearch.org/software/preseq/)
+* [MultiQC](https://multiqc.info/)
+* [BWA](http://bio-bwa.sourceforge.net/)
+* [Qualimap](http://qualimap.bioinfo.cipf.es/)
+* [GATK](https://software.broadinstitute.org/gatk/)
+* [bamUtil](https://genome.sph.umich.edu/wiki/BamUtil)
+* [fastP](https://github.com/OpenGene/fastp)
+
 #### 3.1) Software deps: Docker
 First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
 

docs/usage.md

@@ -7,38 +7,12 @@
 * [Updating the pipeline](#updating-the-pipeline)
 * [Reproducibility](#reproducibility)
 * [Main arguments](#main-arguments)
-    * [`-profile`](#-profile-single-dash)
-        * [`docker`](#docker)
-        * [`awsbatch`](#awsbatch)
-        * [`standard`](#standard)
-        * [`binac`](#binac)
-        * [`cfc`](#cfc)
-        * [`uzh`](#uzh)
-        * [`none`](#none)
-    * [`--reads`](#--reads)
-    * [`--singleEnd`](#--singleend)
-* [Reference Genomes](#reference-genomes)
-    * [`--genome`](#--genome)
-    * [`--fasta`](#--fasta)
 * [Job Resources](#job-resources)
 * [Automatic resubmission](#automatic-resubmission)
 * [Custom resource requests](#custom-resource-requests)
 * [AWS batch specific parameters](#aws-batch-specific-parameters)
-    * [`-awsbatch`](#-awsbatch)
-    * [`--awsqueue`](#--awsqueue)
-    * [`--awsregion`](#--awsregion)
 * [Other command line parameters](#other-command-line-parameters)
-    * [`--outdir`](#--outdir)
-    * [`--email`](#--email)
-    * [`-name`](#-name-single-dash)
-    * [`-resume`](#-resume-single-dash)
-    * [`-c`](#-c-single-dash)
-    * [`--max_memory`](#--max_memory)
-    * [`--max_time`](#--max_time)
-    * [`--max_cpus`](#--max_cpus)
-    * [`--plaintext_emails`](#--plaintext_emails)
-    * [`--sampleLevel`](#--sampleLevel)
-    * [`--multiqc_config`](#--multiqc_config)
+* [Adjustable parameters for nf-core/eager](#adjustable-parameters-for-nf-coreeager)
 
 ## General Nextflow info
 Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through `screen` / `tmux` or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.
@@ -116,7 +90,6 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 * `test`
     * A profile with a complete configuration for automated testing
     * Includes links to test data so needs no other parameters
->>>>>>> TEMPLATE
 * `none`
     * No configuration at all. Useful if you want to build your own config from scratch and want to avoid loading in the default `base` config profile (not recommended).
 
@@ -155,9 +128,18 @@ A normal glob pattern, enclosed in quotation marks, can then be used for `--read
 
 ## Reference Genomes
 
-The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
+### `--fasta`
+If you prefer, you can specify the full path to your reference genome when you run the pipeline:
+
+```bash
+--fasta '[path to Fasta reference]'
+```
+> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`.
 
 ### `--genome` (using iGenomes)
+
+The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
+
 There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.
 
 You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:
@@ -189,14 +171,6 @@ params {
 }
 ```
 
-### `--fasta`
-If you prefer, you can specify the full path to your reference genome when you run the pipeline:
-
-```bash
---fasta '[path to Fasta reference]'
-```
-> If you don't specify appropriate `--bwa_index`, `--fasta_index` parameters, the pipeline will create these indices for you automatically. Note, that saving these for later has to be turned on using `--saveReference`.
-
 ### `--bwa_index`
 
 Use this to specify a previously created BWA index. This saves time in pipeline execution and is especially advised when running multiple times on the same cluster system for example. You can even add a resource specific profile that sets paths to pre-computed reference genomes, saving even time when specifying these.

main.nf

@@ -26,17 +26,18 @@ def helpMessage() {
 
     Mandatory arguments:
       --reads                       Path to input data (must be surrounded with quotes)
-      -profile                      Hardware config to use. docker / aws
+      -profile                      Hardware config to use (e.g. standard, docker, singularity, conda, aws). Ask your system admin if unsure, or check documentatoin.
+      --singleEnd                   Specifies that the input is single end reads (required if not pairedEnd)
+      --pairedEnd                   Specifies that the input is paired end reads (required if not singleend)
+      --fasta                       Path to Fasta reference (required if not iGenome reference)
+      --genome                      Name of iGenomes reference (required if not fasta reference)
 
-    Options:
-      --genome                      Name of iGenomes reference
-      --singleEnd                   Specifies that the input is single end reads
+    Input Data Additional Options:
       --snpcapture                  Runs in SNPCapture mode (specify a BED file if you do this!)
       --udg                         Specify that your libraries are treated with UDG
       --udg_type                    Specify here if you have UDG half treated libraries, Set to 'Half' in that case
 
     References                      If not specified in the configuration file or you wish to overwrite any of the references.
-      --fasta                       Path to Fasta reference
       --bwa_index                   Path to BWA index
       --bedfile                     Path to BED file for SNPCapture methods
       --seq_dict                    Path to sequence dictionary file
@@ -54,8 +55,8 @@ def helpMessage() {
       --complexity_filter_poly_g_min    Specify poly-g min filter (default: 10) for filtering
     
     Clipping / Merging
-      --clip_forward_adaptor        Specify adapter to be clipped off (forward)
-      --clip_reverse_adaptor        Specify adapter to be clipped off (reverse)
+      --clip_forward_adaptor        Specify adapter sequence to be clipped off (forward)
+      --clip_reverse_adaptor        Specify adapter sequence to be clipped off (reverse)
       --clip_readlength             Specify read minimum length to be kept for downstream analysis
       --clip_min_read_quality       Specify minimum base quality for not trimming off bases
       --min_adap_overlap            Specify minimum adapter overlap