$ 
for sequence in */sequence.md
do
(
cd $(dirname $sequence)
pandoc --verbose --from markdown --to pdf --output sequence.pdf sequence.md
)
done
pdftk */sequence.pdf cat output sequences.pdf
pandoc: sequence.md: withBinaryFile: does not exist (No such file or directory)
Error: Unable to find file.
Error: Failed to open input PDF file: 
   */sequence.pdf
Errors encountered.  No output created.
Done.  Input errors, so no output created.