MissingInputException when merging with 0.7.2

[danilexn]

When I try to merge two samples with spacemake 0.7.2, I first run:

spacemake projects merge_samples \
--merged_project_id <project> --merged_sample_id <sample_merged> \
--project_id_list <project> \
--sample_id_list <sample_a> <sample_b> 

(the IDs were replaced by )

Then, when running spacemake run, it exits upon the following exception:

WorkflowError:
MissingInputException: Missing input files for rule symlinks:
NO_BAM_SYMLINKS_for_projects/<project>/processed_data/<sample_merged>/illumina/complete_data/unaligned_bc_tagged.bam
WorkflowError:
    MissingInputException: Missing input files for rule link_raw_reads:
    none
    MissingInputException: Missing input files for rule demultiplex_data:

[nukappa]

I just tested this with 0.7.2 and the following works:

spacemake projects merge_samples \
--merged_project_id <project> \
--merged_sample_id <sample_merged> \
--sample_id_list <sample_a> <sample_b>

The only difference is that I omit project_id_list.

I don't see docs for the merge_samples command rn, but you can use either the project_list_id OR the sample_list_id and it will do what's supposed to.

[nukappa]

I think this was closed prematurely by merging the PR, but should probably be a problem.