amend _alignment_command() to allow creation and interrogation of def… #542
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…initions and p4_params without requiring file creation
generate method's second parameter $mode can take three values:
GENERATE_MODE_DEFAULT => default, generate all files
GENERATE_MODE_NOWRITE => no files written by generate()
GENERATE_MODE_DRY_RUN => only composition files written by generate()
Example:
my $sa = npg_pipeline::function::seq_alignment->new(runfolder_path => q[runfolder], recalibrated_path => q[recal], repository => q[repository], conf_path => q[config],);
my $defs = $sa->generate(q[analysis], $npg_pipeline::function::seq_alignment::GENERATE_MODE_NOWRITE);
print join qq[\n], keys %{$sa->p4_params};
dozy
force-pushed
the
nowrite_alignment_command
branch
from
8f4bd07
to
be39d4b
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
…initions and p4_params without requiring file creation
generate method's second parameter $mode can take three values:
GENERATE_MODE_DEFAULT => default, generate all files
GENERATE_MODE_NOWRITE => no files written by generate()
GENERATE_MODE_DRY_RUN => only composition files written by generate()
Example:
my $sa = npg_pipeline::function::seq_alignment->new(runfolder_path => q[runfolder], recalibrated_path => q[recal], repository => q[repository], conf_path => q[config],);
my $defs = $sa->generate(q[analysis], $npg_pipeline::function::seq_alignment::GENERATE_MODE_NOWRITE);
print join qq[\n], keys %{$sa->p4_params};