Fix bug in SIF generation for replicated blanks

[AmandaBirmingham]

• centralize string operations and identification of blanks
• fix creation of sample information files for blanks from sample sheets with replicates: use original blank names (without replicate destination well suffix) rather than replicate blank name

[Copilot]

Pull Request Overview

This PR fixes SIF generation for replicated blanks by centralizing blank identification and ensuring original blank names (without replicate suffixes) are used.

• Refactored generate_sample_info_files to take a list of dereplicated input file paths and dedupe controls.
• Propagated dereplicated_input_file_paths through GenPrepFileJob, Assays, and Workflows.
• Extended tests with demultiplexed sample‐sheet fixtures and helper logic for multiple replicates with/without context.

Reviewed Changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_Pipeline.py	Updated tests to call generate_sample_info_files with lists, added helper for multi-replicate scenarios
tests/data/good_sheet_w_replicates*demux*.csv	New demultiplexed CSV fixtures covering 3, 2, and 1 replicate cases
tests/data/good_sheet_w_replicates_and_context*demux*.csv	New demux + context fixtures for multiple project mappings
src/sequence_processing_pipeline/Pipeline.py	Changed generate_sample_info_files signature to accept file paths list and drop duplicate controls
src/sequence_processing_pipeline/GenPrepFileJob.py	Stored dereplicated_input_file_paths after demuxing sample sheets
src/qp_klp/Workflows.py	Updated generate_sifs and replaced blank filtering to use new method
src/qp_klp/Assays.py	Converted _replace_tube_ids_w_sample_names to instance method and integrated pipeline state

Comments suppressed due to low confidence (4)

src/sequence_processing_pipeline/Pipeline.py:612

• [nitpick] Changing this signature to require a list breaks backward compatibility. Consider giving dereplicated_input_file_paths a default value of None and falling back to the single input file (or previous behavior) when not provided.

    def generate_sample_info_files(self, dereplicated_input_file_paths):

tests/data/good_sheet_w_replicates_and_context_demux_3.csv:48

• [nitpick] Typo in the test fixture: 'Eqiiperiment' should likely be 'Experiment' to match intended field naming.

TMI_10317,10317,False,AACC,GGTT,False,Knight Lab Kapa HP,Eqiiperiment,,,,

src/qp_klp/Workflows.py:472

• The method sample_is_a_blank does not match the pattern used elsewhere (e.g., sample_name_is_blank). This will cause an AttributeError at runtime. Use the correct method name sample_name_is_blank or delegate to the shared is_blank utility.

                       not self.pipeline.sample_sheet.sample_is_a_blank(smpl)}

tests/test_Pipeline.py:518

• [nitpick] Helper methods typically start with _ and are not collected by test runners - consider renaming to clarify that it is not a standalone test and document its purpose.

    def _help_test_generate_sample_information_files_with_multiple_preps(

[antgonza]

This looks to me but I'm a little concern about not testing in qiita-rc before merge/deploy; what do you think?

[AmandaBirmingham]

No, I don't think it would be a good idea to try to get it in to the deploy so close to the wire. But I would like to get it into main soon so we could test it in qiita-rc on some of our known problem cases :)

[antgonza]

Can you pull from master to update this PR? Thank you.

[antgonza]

I just did another pass here and the only comment is that the new tests sample-sheets have "Sample_Project" need to be updated to not contain names.

[antgonza]

Nice, thank you very much!