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update manifest4study file discrimination regex #187

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merged 2 commits into from
Jun 28, 2021
Merged

update manifest4study file discrimination regex #187

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7cc02b9
update manifest4study file discrimination regex
jmtcsngr Jun 22, 2021
f572672
add example patterns for regex in Changes
jmtcsngr Jun 23, 2021
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6 changes: 6 additions & 0 deletions Changes
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Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
LIST OF CHANGES

- update regex to discriminate crams to consider in manifest4study bin.
regex will look for filename patterns including:
- xxxxx#z.cram
- xxxxx_y#z.cram
- xxxxx_y-y#z.cram

release 44.1.0
- inital ml warehouse run data loader for pacbio data
- move from Travis CI to GitHub Actions
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2 changes: 1 addition & 1 deletion bin/npg_manifest4study
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Expand Up @@ -254,7 +254,7 @@ sub _uploaded_files {

while (<$fh>) {
##no critic (RegularExpressions::RequireExtendedFormatting RegularExpressions::ProhibitEscapedMetacharacters ProhibitComplexRegexes)
if ( m{(\S+/(\d+)/((\d+)(?:_(\d))?#(\d+)[.]cram)):.*Hash \(md5\):\s+(\S+)}sm ) {
if ( m{(\S+/(\d+)/((\d+)(?:_(\d)(?:-\d)*)?#(\d+)[.]cram)):.*Hash \(md5\):\s+(\S+)}sm ) {
my $path = $1;
my $sample = $2;
my $file_name = $3;
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