refactor: Remove file names (#4)

* chore: remove direct mention of file names

* refactor: remove mention of file names in usage functions

JobSubmission/BS-Seq/1_binarize_WGBS_data.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-1_binarize_WGBS_data.sh
+$(basename "$0")
 ================================================================================
 Purpose: Create binary files for dense and sparse regions of methylation 
 from whole genome bisulphite sequencing bed files. Bed files are expected to be 

JobSubmission/BS-Seq/2_binarize_oxBS_5mC_data.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-2_binarize_oxBS_5mC_data.sh
+$(basename "$0")
 ================================================================================
 Purpose: Create binary files for dense and sparse regions of 5mC from 
 oxidative bisulphite sequencing bed files. Bed files are expected to be in the 

JobSubmission/BS-Seq/3_binarize_pure_5hmC_data.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-3_binarize_pure_5hmC_data.
+$(basename "$0")
 ================================================================================
 Purpose: Create binary files for dense and sparse regions of 5hmc using a
 combination of whole genome bisulphite sequencing and oxidative bisulphite

JobSubmission/ONT/1_purify_reads.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-1_purify_reads.sh
+$(basename "$0")
 ================================================================================
 Purpose: Filters input ONT file on sites that are significantly methylated
 Optional argument: -c -> train erroneous reads probability on CpGs in CGIs only

JobSubmission/ONT/2_binarize_reads.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-2_binarize_reads.sh
+$(basename "$0")
 ================================================================================
 Purpose: Turns processed ONT data into dense and sparsed ChromHMM compliable
 binarized data.

JobSubmission/Peaks_to_Binary/1_convert_MACS_to_binary.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-1_convert_MACS_to_binary.sh
+$(basename "$0")
 ================================================================================
 Purpose: Converts narrow peak or broad peaks to binary format for chromHMM
 Author: Sam Fletcher

JobSubmission/supplementary/a_erroneous_rate_plot.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-a_erroneous_rate_plot.sh
+$(basename "$0")
 ================================================================================
 Purpose: Outputs plots that show how approximated erroneous methylation call 
 probability changes with read depth/methylation percent thresholds.

JobSubmission/supplementary/b_CpG_robustness.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-b_CpG_robustness.sh
+$(basename "$0")
 ================================================================================
 Purpose: Calculates the correlation of percent methylation seen in local 
 clusters of CpGs. High correlation suggests robustness in basecalling.

JobSubmission/supplementary/c_WGBS_comparison.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-c_WGBS_comparison.sh
+$(basename "$0")
 ================================================================================
 Purpose: Creates several plots comparing a two bed files. One for ONT, the 
 other for WGBS data.

JobSubmission/supplementary/d_oxBS_comparison.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-d_oxBS_comparison.sh
+$(basename "$0")
 ================================================================================
 Purpose: Creates several plots comparing a two bed files. One for ONT, the 
 other for oxBS data.

JobSubmission/supplementary/e_change_bin_size.sh

@@ -14,7 +14,7 @@
 usage() {
 cat <<EOF
 ================================================================================
-e_change_bin_size.sh
+$(basename "$0")
 ================================================================================
 Purpose: Converts a binary file from one bin size to another.
 WARNING: For best results, the new bin size should be smaller than the original

config-setup.txt

@@ -97,17 +97,17 @@ input_MACS_file=
 bed_file_location="${ONT_bed_file_location}"
 
 ## ......................... ##
-## a_erroneous_rate_plot.sh  ##
+##   Plotting error rates    ##
 ## ......................... ##
 
 # In some datasets, the maximum value for the read depth of a single site
 # can be in the thousands. However, most sites are well below this number,
 # putting a maximum value here helps with interpretability of plots.
 max_N_value=750
 
-## .................... ##
-## b_CpG_robustness.sh  ##
-## .................... ##
+## .................. ##
+##   CpG robustness   ##
+## .................. ##
 
 # Minimum distance between CpGs that you would consider 'close proximity'
 min_distance=0