Error when adding samples to bundle

[seallard]

@fevac Has the behaviour for housekeeper changed? I used to be able to store subsampled samples with:

housekeeper add bundle $down_sample_id
housekeeper add file -b $down_sample_id -t fastq $down_fastq_r1
housekeeper add file -b $down_sample_id -t fastq $down_fastq_r2
housekeeper include $down_sample_id

Now it fails on the second command because the folder is housekeeper is not created. FileNotFoundError: [Errno 2] No such file or directory

@peterpru The command:

housekeeper add file -t fastq -b newlyrapidglider /home/proj/stage/rare-disease/cases/mintkrill/downsampling/HGV2JDMXY_ACC10479A49_S104_L001_R1_001.fastq.gz

[SofiaOtero]

The commands work in this order:

housekeeper add bundle $down_sample_id
housekeeper include $down_sample_id
housekeeper add file -b $down_sample_id -t fastq $down_fastq_r1
housekeeper add file -b $down_sample_id -t fastq $down_fastq_r2

An option could be to include the bundle in the housekeeper add bundlecommand.

[islean]

Just a question - was it intended to add a stage file in the production environment?

[peterpru]

Just a question - was it intended to add a stage file in the production environment?

For my code, yes. I had decompressed and downsampled fastq files in stage, which I wanted to save in housekeeper, to use in production after.

Regarding the comment from Sofia, before this error, the commands were the other way around, where include was done last, as also shown in the downsampling page of atlas: https://atlas.scilifelab.se/production/data_analysis/supporting_procedures/downsampling/

[henrikstranneheim]

If it is going to be used in production then everything should have been done in the production context. And then you copy the database and the file(s) you created to stage (if you want test something). Avoid doing stage to production as it is bound to cause issues.

[peterpru]

If it is going to be used in production then everything should have been done in the production context. And then you copy the database and the file(s) you created to stage (if you want test something). Avoid doing stage to production as it is bound to cause issues.

I will keep that in mind for the future. 👍 I will downsample in a different folder.

[Vince-janv]

Decision:

• Make houskeeper add bundle create the housekeeper-bundles/ folder

[islean]

Fixed today in #136.