Removing samples from analysis (sample.tsv) simplified?!

[the-eon-flux]

Background:
I am currently doing multiple metagenome assemblies on different datasets. Probably there are many other users who also may use ATLAS on multiple occasions. As recommended in multiple issues/errors I often remove samples at different stages of ATLAS. Some samples fail at QC, some at assembly, and so forth.

My suggestion:

• To remove the samples from analysis, can we just comment out sample IDs in the samples.tsv file, instead of removing the sample ID rows from the file?

SampleID	Reads_raw_R1	Reads_raw_R2	BinGroup
Sample1	path_to_fastq/sample1_1.fastq.gz	path_to_fastq/sample1_2.fastq.gz	S1
#Sample2	path_to_fastq/sample2_1.fastq.gz	path_to_fastq/sample2_2.fastq.gz	S1

• Or can there be an additional column in the metadata file (sample.tsv) that would indicate if the sample needs to be included in the analysis or not?

Include sample?	SampleID	Reads_raw_R1	Reads_raw_R2	BinGroup
Y	Sample1	path_to_fastq/sample1_1.fastq.gz	path_to_fastq/sample1_2.fastq.gz	S1
N	Sample2	path_to_fastq/sample2_1.fastq.gz	path_to_fastq/sample2_2.fastq.gz	S1

Reason: This is just an idea that would make the user(s) life easier. We can discuss the reasons for this being completely absurd or not feasible. Also, some of the commercial s/w (GUI-based) often have this checkbox to include the sample in the analysis or not. They revolve the analysis around their metadata file. But for our purposes maybe the samples.tsv file can be used to do the same?

To further entertain this idea, in the far future, maybe, the user/atlas can add text comments for failed/excluded samples in an additional column that indicates a reason for sample exclusion.
For eg.

• Bad reads,
• no contigs after assemblies,
• Maxbin cannot bin (no marker genes found)

This way we know which samples were excluded from each module/step for a given dataset. This column can be completely ignored by the ATLAS workflow (this is just for the user).

Or, maybe can this be exported/added as a table in a report or in atlas_analyze? A table/plot indicating which samples failed at what stage.

Your thoughts on this?!