Merge branch 'ar/improve-helps' into 'master'

[qol] Adds short helps to all commands when no arguments are provided

See merge request machine-learning/modkit!148

src/bin/main.rs

@@ -4,6 +4,8 @@ use mod_kit::commands::Commands;
 
 #[derive(Parser)]
 #[command(version)]
+/// Modkit is a bioinformatics tool for working with modified bases from Oxford
+/// Nanopore
 struct Cli {
     #[command(subcommand)]
     command: Commands,

src/commands.rs

@@ -148,6 +148,7 @@ fn get_sampling_options(
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct Adjust {
     /// BAM file to collapse mod call from. Can be a path to a file or one of
     /// `-` or `stdin` to specify a stream from standard input.
@@ -308,6 +309,7 @@ fn parse_percentiles(
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct SampleModBaseProbs {
     /// Input BAM with modified base tags. If a index is found
     /// reads will be sampled evenly across the length of the
@@ -575,6 +577,7 @@ impl SampleModBaseProbs {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct ModSummarize {
     /// Input modBam, can be a path to a file or one of `-` or
     /// `stdin` to specify a stream from standard input.
@@ -850,6 +853,7 @@ impl ModSummarize {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct MotifBed {
     /// Input FASTA file
     fasta: PathBuf,
@@ -887,6 +891,7 @@ impl ModMode {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct Update {
     /// BAM to update modified base tags in. Can be a path to a file or one of
     /// `-` or `stdin` to specify a stream from standard input.
@@ -1035,6 +1040,7 @@ impl Update {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct CallMods {
     // running args
     /// Input BAM, may be sorted and have associated index available. Can be a

src/dmr/subcommands.rs

@@ -51,6 +51,7 @@ impl BedMethylDmr {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct PairwiseDmr {
     /// Bgzipped bedMethyl file for the first (usually control) sample. There
     /// should be a tabix index with the same name and .tbi next to this
@@ -354,6 +355,7 @@ impl PairwiseDmr {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct MultiSampleDmr {
     /// Two or more named samples to compare. Two arguments are required <path>
     /// <name>. This option should be repeated at least two times.

src/extract/subcommand.rs

@@ -43,6 +43,7 @@ use crate::util::{
 use crate::writers::TsvWriter;
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct ExtractMods {
     /// Path to modBAM file to extract read-level information from, or one of
     /// `-` or `stdin` to specify a stream from standard input. If a file

src/pileup/subcommand.rs

@@ -38,6 +38,7 @@ use crate::writers::{
 };
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct ModBamPileup {
     // running args
     /// Input BAM, should be sorted and have associated index available.
@@ -794,6 +795,7 @@ enum Presets {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct DuplexModBamPileup {
     // running args
     /// Input BAM, should be sorted and have associated index available.

src/repair_tags.rs

@@ -22,6 +22,7 @@ use std::path::PathBuf;
 use std::sync::Arc;
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct RepairTags {
     /// Donor modBAM with original MM/ML tags. Must be sorted by read name.
     #[arg(long, short = 'd', alias = "donor")]

src/validate/subcommand.rs

@@ -595,6 +595,7 @@ fn print_table(status_probs: &StatusProbs, show_percentages: bool) {
 }
 
 #[derive(Args)]
+#[command(arg_required_else_help = true)]
 pub struct ValidateFromModbam {
     // running args
     // convert to list of bam bed inputs