docs: remove straggler subheader numbers

docs/user-guide/preparing-files.md

@@ -1,37 +1,37 @@
-# 2. Preparing Files
+# Preparing Files
 
 The pipeline is controlled through editing configuration and manifest files. Defaults are found in the /WORKDIR/config and /WORKDIR/manifest directories, after initialization.
 
-## 2.1 Configs
+## Configs
 
 The configuration files control parameters and software of the pipeline. These files are listed below:
 
 - config/config.yaml
 - resources/cluster.yaml
 - resources/tools.yaml
 
-### 2.1.1 Cluster Config
+### Cluster Config
 
-The cluster configuration file dictates the resouces to be used during submission to Biowulf HPC. There are two differnt ways to control these parameters - first, to control the default settings, and second, to create or edit individual rules. These parameters should be edited with caution, after significant testing.
+The cluster configuration file dictates the resources to be used during submission to Biowulf HPC. There are two different ways to control these parameters - first, to control the default settings, and second, to create or edit individual rules. These parameters should be edited with caution, after significant testing.
 
-### 2.1.2 Tools Config
+### Tools Config
 
 The tools configuration file dictates the version of each software or program that is being used in the pipeline.
 
-### 2.1.3 Config YAML
+### Config YAML
 
 There are several groups of parameters that are editable for the user to control the various aspects of the pipeline. These are :
 
 - Folders and Paths
-  - These parameters will include the input and ouput files of the pipeline, as well as list all manifest names.
+  - These parameters will include the input and output files of the pipeline, as well as list all manifest names.
 - User parameters
   - These parameters will control the pipeline features. These include thresholds and whether to perform processes.
 - References
   - These parameters will control the location of index files, spike-in references, adaptors and species calling information.
 
-#### 2.1.3.1 User Parameters
+#### User Parameters
 
-##### 2.1.3.1.1 (Spike in Controls)
+##### Spike in Controls
 
 The pipeline allows for the use of a species specific spike-in control, or the use of normalization via library size. The parameter `spikein_genome` should be set to the species term used in `spikein_reference`.
 
@@ -62,19 +62,19 @@ spikein_reference:
 If it's determined that the amount of spike-in is not sufficient for the run, a library normaliaztion can be performed.
 
 1. Complete a CARLISLE run with spike-in set to "Y". This will allow for the complete assessment of the spike-in.
-2. Run inital QC analysis on the output data
+2. Run initial QC analysis on the output data
 3. Add the alignment_stats dir to the configuration file.
 4. Re-run the CARLISLE pipeline
 
-##### 2.1.3.1.2 Duplication Status
+##### Duplication Status
 
 Users can select duplicated peaks (dedup) or non-deduplicated peaks (no_dedup) through the user parameter.
 
 ```
 dupstatus: "dedup, no_dedup"
 ```
 
-##### 2.1.3.1.3 Peak Caller
+##### Peak Caller
 
 Three peak callers are available for deployment within the pipeline, with different settings deployed for each caller.
 
@@ -112,14 +112,14 @@ A complete list of the available peak calling parameters and the recommended lis
 ### peaktype: "macs2_narrow, macs2_broad, seacr_norm_stringent, seacr_norm_relaxed, seacr_non_stringent, seacr_non_relaxed, gopeaks_narrow, gopeaks_broad"
 ```
 
-##### 2.1.3.1.3.1 Macs2 additional option
+##### Macs2 additional option
 
 MACS2 can be run with or without the control. adding a control will increase peak specificity
 Selecting "Y" for the `macs2_control` will run the paired control sample provided in the sample manifest
 
-##### 2.1.3.1.4 Quality Tresholds
+##### Quality Tresholds
 
-Thresholds for quality can be controled through the `quality_tresholds` parameter. This must be a list of comma separated values. minimum of numeric value required.
+Thresholds for quality can be controlled through the `quality_thresholds` parameter. This must be a list of comma separated values. minimum of numeric value required.
 
 - default MACS2 qvalue is 0.05 https://manpages.ubuntu.com/manpages/xenial/man1/macs2_callpeak.1.html
 - default GOPEAKS pvalue is 0.05 https://github.com/maxsonBraunLab/gopeaks/blob/main/README.md
@@ -130,7 +130,7 @@ Thresholds for quality can be controled through the `quality_tresholds` paramete
 quality_thresholds: "0.1, 0.05, 0.01"
 ```
 
-#### 2.1.3.2 References
+#### References
 
 Additional reference files may be added to the pipeline, if other species were to be used.
 
@@ -144,14 +144,14 @@ The following information must be included:
 1. regions: "list of regions to be included; IE chr1 chr2 chr3"
 2. macs2_g: "macs2 genome shorthand; IE mm IE hs"
 
-## 2.2 Preparing Manifests
+## Preparing Manifests
 
-There are two manifests, one which required for all pipeliens and one that is only required if running a differential analysis. These files describe information on the samples and desired contrasts. The paths of these files are defined in the snakemake_config.yaml file. These files are:
+There are two manifests, one which required for all pipelines and one that is only required if running a differential analysis. These files describe information on the samples and desired contrasts. The paths of these files are defined in the snakemake_config.yaml file. These files are:
 
 - samplemanifest
 - contrasts
 
-### 2.2.1 Samples Manifest (REQUIRED)
+### Samples Manifest (REQUIRED)
 
 This manifest will include information to sample level information. It includes the following column headers:
 
@@ -173,7 +173,7 @@ An example sampleManifest file is shown below:
 | HN6_H3K4me3                     | 2               | N         | HN6_IgG_rabbit_negative_control | 1                      | PIPELINE_HOME/.test/HN6_H3K4me3_2.R1.fastq.gz                     | PIPELINE_HOME/.test/HN6_H3K4me3_2.R2.fastq.gz                     |
 | HN6_IgG_rabbit_negative_control | 1               | Y         | -                               | -                      | PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz | PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz |
 
-### 2.2.2 Contrast Manifest (OPTIONAL)
+### Contrast Manifest (OPTIONAL)
 
 This manifest will include sample information to performed differential comparisons.