Commit 63f74c6e authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

Merge branch 'feature-a/2259-shouldvdj-in-one' into 'dev'

Feature a/2259 shouldvdj in one

See merge request !411
parents 2208ab8b 0c680733
Pipeline #64127 failed with stages
in 17 minutes and 31 seconds
......@@ -98,7 +98,7 @@ shouldvdj_with_rc:
$(SHOULD_VDJ_TO_TAP) -r $(SHOULD_VDJ)
shouldvdj_with_rc_merged:
cat $(SHOULD_VDJ) > should-vdj-tests/should-vdj.merged.fa
awk 1 $(SHOULD_VDJ) > should-vdj-tests/should-vdj.merged.fa
$(SHOULD_VDJ_TO_TAP) -r should-vdj-tests/should-vdj.merged.fa
# When the global test suite is passing, individual failed tests (tagged with BUG or BUG-LOCUS in the *.should-vdj.fa files)
......
......@@ -249,7 +249,7 @@ def header_igblast_results(ff_fasta, ff_igblast):
### Vidjil
VIDJIL_FINE = '{directory}/vidjil-algo -X 100 --header-sep "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_FINE = '{directory}/vidjil-algo --header-sep "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_KMER = '{directory}/vidjil-algo -w 20 --header-sep "#" -b out -c windows -uuuU -2 -g {directory}/germline/homo-sapiens.g %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa >> %s'
def should_results_from_vidjil_output(f_log):
......
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