Validation of test example

The reference results to compare to:

truth=/cbc/henrik/LG3_Pipeline/tests/Patient157t-truth-20180914

Existence of folders and files

The following output should be empty (because all files should exist):

diff -u <(cd ${truth}; tree -I '*_2018*' output) <(tree -I '*_2018*' output)

_run_Trim

The following output should be empty (because all files should be of identical sizes):

path=output
diff <(cd ${truth}; tree ${path}/Z00*t-trim) -u <(tree ${path}/Z00*t-trim)
diff <(cd ${truth}; du -b ${path}/Z00*t-trim/*) -u <(du -b ${path}/Z00*t-trim/*)

_run_Align_gz

The following output should be empty (because all files should be of identical sizes):

path=output/LG3/exomes
diff <(cd ${truth}; tree ${path}) -u <(tree ${path})
diff -u <(cd ${truth}; du -b ${path}/Z00*t/*) <(du -b ${path}/Z00*t/*)

_run_Recal

The following output should be empty (because all files should be of the "human-readable" size and BAI files of identical size):

path=output/LG3/exomes_recal
diff -u <(cd ${truth}; tree ${path}) <(tree ${path})
diff -u <(cd ${truth}; du -h ${path}/Patient*t/*) <(du -h ${path}/Patient*t/*)
diff -u <(cd ${truth}; du -h ${path}/Patient*t/germline/*) <(du -h ${path}/Patient*t/germline/*)
diff -u <(cd ${truth}; du -b ${path}/Patient*t/*.bai) <(du -b ${path}/Patient*t/*.bai)

_run_Pindel

The following output should be empty (because all files should be of the "human-readable" size):

path=output/LG3/pindel
diff -u <(cd ${truth}; tree ${path}) <(tree ${path})
diff -u <(cd ${truth}; wc -l ${path}/Patient*t.pindel.cfg) <(wc -l ${path}/Patient*t.pindel.cfg)
diff -u <(cd ${truth}; du -h ${path}/Patient*t_pindel/*) <(du -h ${path}/Patient*t_pindel/*)

_run_MutDet

The following output should be empty (because all files should be of the "human-readable" size):

path=output/LG3/mutations
diff -u <(cd ${truth}; tree -I '*.bed' ${path}) <(tree -I '*.bed' ${path})
diff -u <(cd ${truth}; du -h ${path}/Patient*t_mutect/* | grep -vF .bed) <(du -h ${path}/Patient*t_mutect/* | grep -vF .bed)

When _run_PostMut_, which produce BED files, has been, we can do a full comparison:

diff -u <(cd ${truth}; tree ${path}) <(tree ${path})
diff -u <(cd ${truth}; du -h ${path}/Patient*t_mutect/*) <(du -h ${path}/Patient*t_mutect/*)

Comment: There could be a minor difference in WIG content:

for ff in ${path}/Patient*t_*/*.wig; do diff -U 0 ${truth}/${ff} ${ff}; done
--- /cbc/henrik/LG3_Pipeline/tests/Patient157t-truth-20180914/output/LG3/mutations/Patient157t_mutect/NOR-Z00599t__TUM-Z00600t.snvs.coverage.mutect.wig      2018-09-15 14:09:40.391889978 -0700
+++ output/LG3/mutations/Patient157t_mutect/NOR-Z00599t__TUM-Z00600t.snvs.coverage.mutect.wig   2018-09-18 15:34:03.471534304 -0700
@@ -12590739 +12590739 @@
-0
+1

_run_PostMut

The following output should be empty (because all files should be of the "human-readable" size):

path=output/LG3/MAF
diff -u <(cd ${truth}; tree ${path}) <(tree ${path})
diff -u <(cd ${truth}; du -h ${path}/Patient*t_*/*) <(du -h ${path}/Patient*t_*/*)

and

path=output/LG3/MutInDel
diff -u <(cd ${truth}; tree ${path}) <(tree ${path})
diff -u <(cd ${truth}; du -h ${path}/*) <(du -h ${path}/*)
diff -u ${truth}/${path}/Patient157t.R.mutations ${path}/Patient157t.R.mutations