DOC: update paper

paper/paper.md

@@ -68,6 +68,7 @@ A user can start the analysis by running the `metacoag` subcommand to bin a meta
 ### Inputs
 
 The following inputs are required to run the `metacoag` subcommand.
+
 * Contigs
 * Assembly graph file(s)
 * Coverage of contigs - can be obtained by running a coverage calculation tool such as CoverM [https://github.com/wwood/CoverM](https://github.com/wwood/CoverM) or Koverage [@Roach:2024]
@@ -77,6 +78,7 @@ The assembly graph files can vary depending on the assembler used to generate th
 ### Outputs
 
 The following outputs will be generated by the `metacoag` subcommand.
+
 * A delimited text file containing the contig identifier and bin identifier for each binned contig
 * `.fasta` files for each bin
 
@@ -105,6 +107,7 @@ This formatted binning result from MetaCoAG can be improved by providing to Grap
 ### Inputs
 
 The following inputs are required to run the `graphbin` subcommand.
+
 * Contigs file
 * Assembly graph file(s) - can vary depending on the assembler used to generate the contigs (refer to inputs under 'metacoag')
 * A delimited text file containing the initial binning result
@@ -113,6 +116,7 @@ The following inputs are required to run the `graphbin` subcommand.
 ### Outputs
 
 The following outputs will be generated by the `graphbin` subcommand.
+
 * A delimited text file containing the contig identifier and bin identifier for each binned contig
 * `.fasta` files for each bin
 
@@ -123,13 +127,15 @@ This formatted binning result can be improved by providing to GraphBin2 [@Mallaw
 ### Inputs
 
 The following inputs are required to run the `graphbin2` subcommand.
+
 * Contigs file
 * Assembly graph file(s) - can vary depending on the assembler used to generate the contigs (refer to inputs under 'metacoag')
 * A delimited text file containing the initial binning result
 
 ### Outputs
 
 The following outputs will be generated by the `graphbin2` subcommand.
+
 * A delimited text file containing the contig identifier and bin identifier for each binned contig
 * `.fasta` files for each bin
 
@@ -143,6 +149,7 @@ The initial MetaCoAG binning result and the refined binning result can be visual
 ### Inputs
 
 The following inputs are required to run the `visualise` subcommand.
+
 * Contigs file
 * Assembly graph file(s) - can vary depending on the assembler used to generate the contigs (refer to inputs under 'metacoag')
 * A delimited text file containing the initial binning result
@@ -151,6 +158,7 @@ The following inputs are required to run the `visualise` subcommand.
 ### Outputs
 
 The following outputs will be generated by the `visualise` subcommand.
+
 * Figure of the assembly graph with the initial binning result
 * Figure of the assembly graph with the refined binning result
 
@@ -175,6 +183,7 @@ __ARI__ = $\frac{\sum_{k,s}\binom{a_{ks}}{2}-t_3}{\frac{1}{2}(t_1+t_2)-t_3}$ $wh
 ### Inputs
 
 The following inputs are required to run the `evaluate` subcommand.
+
 * Delimited text file for the ground truth
 * Delimited text file for the binning result