Here's how you can specify that with find:

find . -type f -name "*_peaks.bed" ! -path "./tmp/*" ! -path "./scripts/*"

Explanation:

• find . - Start find from current working directory (recursively by default)
• -type f - Specify to find that you only want files in the results
• -name "*_peaks.bed" - Look for files with the name ending in _peaks.bed
• ! -path "./tmp/*" - Exclude all results whose path starts with ./tmp/
• ! -path "./scripts/*" - Also exclude all results whose path starts with ./scripts/

Testing the Solution:

$ mkdir a b c d e$ touch a/1 b/2 c/3 d/4 e/5 e/a e/b$ find . -type f ! -path "./a/*" ! -path "./b/*"./d/4./c/3./e/a./e/b./e/5

You were pretty close, the -name option only considers the basename, where as -path considers the entire path =)

Here is one way you could do it...

find . -type f -name "*_peaks.bed" | egrep -v "^(./tmp/|./scripts/)"

Use

find \( -path "./tmp" -o -path "./scripts" \) -prune -o  -name "*_peaks.bed" -print

or

find \( -path "./tmp" -o -path "./scripts" \) -prune -false -o  -name "*_peaks.bed"

or

find \( -path "./tmp" -path "./scripts" \) ! -prune -o  -name "*_peaks.bed"

The order is important. It evaluates from left to right.Always begin with the path exclusion.

Explanation

Do not use -not (or !) to exclude whole directory. Use -prune.As explained in the manual:

−prune    The primary shall always evaluate as  true;  it          shall  cause  find  not  to descend the current          pathname if it is a directory.  If  the  −depth          primary  is specified, the −prune primary shall          have no effect.

and in the GNU find manual:

-path pattern              [...]              To ignore  a  whole              directory  tree,  use  -prune rather than checking              every file in the tree.

Indeed, if you use -not -path "./pathname",find will evaluate the expression for each node under "./pathname".

find expressions are just condition evaluation.

• \( \) - groups operation (you can use -path "./tmp" -prune -o -path "./scripts" -prune -o, but it is more verbose).
• -path "./script" -prune - if -path returns true and is a directory, return true for that directory and do not descend into it.
• -path "./script" ! -prune - it evaluates as (-path "./script") AND (! -prune). It revert the "always true" of prune to always false. It avoids printing "./script" as a match.
• -path "./script" -prune -false - since -prune always returns true, you can follow it with -false to do the same than !.
• -o - OR operator. If no operator is specified between two expressions, it defaults to AND operator.

Hence, \( -path "./tmp" -o -path "./scripts" \) -prune -o -name "*_peaks.bed" -print is expanded to:

[ (-path "./tmp" OR -path "./script") AND -prune ] OR ( -name "*_peaks.bed" AND print )

The print is important here because without it is expanded to:

{ [ (-path "./tmp" OR -path "./script" )  AND -prune ]  OR (-name "*_peaks.bed" ) } AND print

-print is added by find - that is why most of the time, you do not need to add it in you expression. And since -prune returns true, it will print "./script" and "./tmp".

It is not necessary in the others because we switched -prune to always return false.

Hint: You can use find -D opt expr 2>&1 1>/dev/null to see how it is optimized and expanded,
find -D search expr 2>&1 1>/dev/null to see which path is checked.