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Inferring expected files from sample names is just awful #93

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ressy opened this issue Aug 26, 2020 · 0 comments · Fixed by #94
Closed

Inferring expected files from sample names is just awful #93

ressy opened this issue Aug 26, 2020 · 0 comments · Fixed by #94
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enhancement New feature or request
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Version 0.0.4

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@ressy
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ressy commented Aug 26, 2020

Since there isn't a straightforward mapping of sample names to file names, different Illumina programs do that name conversion differently, and duplicate sample names are allowed, we need to switch to using sample numbers and existing files on disk rather than trying to figure out what the files should be named. This can be done internally in the illumina package to start with, with minimal visible changes, before switching the project metadata to be sample-number-based. This change is a first step toward addressing #50.
@ressy ressy added the enhancement New feature or request label Aug 26, 2020
@ressy ressy added this to the Version 0.0.4 milestone Aug 26, 2020
ressy added a commit that referenced this issue Aug 26, 2020
@ressy
For #93: failing tests for new alignment behavior
fb8b60a 
New expected behaior: sample_files_for_num is gone and only
sample_paths_for_num should be used instead; missing filenames are
missing in sample_paths_from_num output rather than present but
nonexistent on disk; filename are loaded only during refresh() rather
than in the filename functions.
ressy added a commit that referenced this issue Aug 26, 2020
@ressy
For #93: add load_sample_filenames util function
b15b13d
ressy added a commit that referenced this issue Aug 26, 2020
@ressy
For #93: parse alignment fastq.gz info from disk
31ec2b2 
Switch from predicting filenames from sample sheet information to
parsing it from the fastq.gz files actually on disk.  The information is
loaded during refresh() rather than in the filename functions.
@ressy ressy mentioned this issue Aug 26, 2020
Merged
@ressy ressy closed this as completed in #94 Aug 26, 2020
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Parse sample file paths from disk ShawHahnLab/umbra
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