Bash Scripting – How to Add Comments for Each Flag on Separate Lines

bashcommand line

I want to write bash scripts that are as self-documentary as possible.

I had an idea that when I execute software with lots of flags, I wanted to split the command into multiple lines, and add a comment at the end of each line, telling what the flag does (info from a man page), like so:

bwa aln \
-n $n \ # -n max #diff (integer) or missing prob under 0.02 err rate (float) [0.04]
-o $o \ # -o maximum number or fraction of gap opens [1]
-e $e \ # -e maximum number of gap extensions, -1 for disabling long gaps [-1]
-i $i \ # -i do not put an indel within integer bp towards the ends [5]
-d $d \ # -d maximum occurrences for extending a long deletion [10]
-l $l \ # -l seed length [32]
-k $k \ # -k maximum differences in the seed [2]
-m $m \ # -m maximum entries in the queue [2000000]
-t $t \ # -t number of threads [1]
-M $M \ # -M mismatch penalty [3]
-O $O \ # -O gap open penalty [11]
-E $E \ # -E gap extension penalty [4]
-R $R \ # -R stop searching when there are >integer equally best hits [30]
-q $q \ # -q quality threshold for read trimming down to 35bp [0]
-f $f \ # -f file to write output to instead of stdout
-B $B \ # -B length of barcode
-L $L \ # -L log-scaled gap penalty for long deletions
-N $N \ # -N non-iterative mode: search for all n-difference hits (slooow)
-I $I \ # -I the input is in the Illumina 1.3+ FASTQ-like format
-b $b \ # -b the input read file is in the BAM format
-0 $0 \ # -0 use single-end reads only (effective with -b)
-1 $1 \ # -1 use the 1st read in a pair (effective with -b)
-2 $2 \ # -2 use the 2nd read in a pair (effective with -b)
-Y $Y \ # -Y filter Casava-filtered sequences
-prefix $prefix \ # -prefix Prefix
-inputfile $inputfile \ # -inputfile Input file (FastQ format)

The problem is that I can not have anything after the \ character (that tells bash that the command continues on next line), and neither can I have the "\" at the end of the line, because then it is treated as part of the comment.

Anybody knows a way to do this, or something similar?

Best Answer

You can evaluate comments before the slash, simply generating empty strings for comments which won't affect your script:

bwa aln \
-n $n `# -n max #diff (integer) or missing prob under 0.02 err rate (float) [0.04]` \
-o $o `# -o maximum number or fraction of gap opens [1]` \
....

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