diff --git a/Changes b/Changes index a8f209dc..6a4f896d 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,9 @@ LIST OF CHANGES --------------- + - The runfolder_path argument is added to the command for the autoqc review + check. See https://github.com/wtsi-npg/npg_qc/pull/869 + release 68.4.0 (2024-08-06) - Ensured mark duplicate method can be inferred for a product with multiple studies (tag zero). diff --git a/lib/npg_pipeline/function/autoqc.pm b/lib/npg_pipeline/function/autoqc.pm index 1f51c0a7..d79aeee0 100644 --- a/lib/npg_pipeline/function/autoqc.pm +++ b/lib/npg_pipeline/function/autoqc.pm @@ -271,8 +271,8 @@ sub _generate_command { $c .= q[ ] . join q[ ], (map {"--qc_in=$_"} (keys %qc_in_roots)); } elsif($check eq q/review/) { - $c .= q{ --qc_in=} . $qc_out_path; - $c .= q{ --conf_path=} . $self->conf_path; + $c .= sprintf q{ --qc_in=%s --conf_path=%s --runfolder_path=%s}, + $qc_out_path, $self->conf_path, $self->runfolder_path; } else { ## default input_files [none?] diff --git a/t/20-function-autoqc.t b/t/20-function-autoqc.t index 157b6a67..8b1a6a7d 100644 --- a/t/20-function-autoqc.t +++ b/t/20-function-autoqc.t @@ -615,13 +615,15 @@ subtest 'review' => sub { my $d = $definitions{'8747:8'}; my $expected_command = q{qc --check=review --rpt_list="8747:8" } . qq{--filename_root=8747_8 --qc_out=$archive_dir/lane8/qc } . - qq{--qc_in=$archive_dir/lane8/qc --conf_path=t/data/release/config/qc_review}; + qq{--qc_in=$archive_dir/lane8/qc --conf_path=t/data/release/config/qc_review } . + qq{--runfolder_path=$rf_path}; is ($d->command, $expected_command, 'correct command for lane-level job'); $d = $definitions{'8747:1:1'}; $expected_command = q{qc --check=review --rpt_list="8747:1:1" } . qq{--filename_root=8747_1#1 --qc_out=$archive_dir/lane1/plex1/qc } . - qq{--qc_in=$archive_dir/lane1/plex1/qc --conf_path=t/data/release/config/qc_review}; + qq{--qc_in=$archive_dir/lane1/plex1/qc --conf_path=t/data/release/config/qc_review } . + qq{--runfolder_path=$rf_path}; is ($d->command, $expected_command, 'correct command for plex-level job'); };