Describe the bug
When using a loom file as input, if the loom file has been generated from ScopeLoomR the pipeline crashes.
To Reproduce
Steps to reproduce the behavior:
Configure with these options:
# Set working directory
WORK_DIR='/staging/leuven/stg_00002/lcb/cbravo/Multiomics_pipeline/analysis/Bravo_EAD_ScoMAP'
# Move to folder and generate config
mkdir -p $WORK_DIR/scripts/rna/vsn
nextflow config vib-singlecell-nf/vsn-pipelines \
-profile loom,single_sample,dm6,scenic,scenic_use_cistarget_motifs,singularity, > $WORK_DIR/scripts/rna/vsn/single_sample_scenic.config
Run using this entry point:
# Run pipeline
mkdir -p $WORK_DIR/output/rna/vsn
cd $WORK_DIR/output/rna/vsn
nextflow -C $WORK_DIR/scripts/rna/vsn/single_sample_scenic.config run vib-singlecell-nf/vsn-pipelines -entry single_sample_scenic
See error:
Error executing process > 'single_sample_scenic:SINGLE_SAMPLE:SC__FILE_CONVERTER (1)'
Caused by:
Process single_sample_scenic:SINGLE_SAMPLE:SC__FILE_CONVERTER (1) terminated with an error exit status (1)
Command error:
Traceback (most recent call last):
File "/user/leuven/313/vsc31305/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/src/utils/bin/sc_file_converter.py", line 256, in
sparse=False
File "/opt/venv/lib/python3.7/site-packages/anndata/readwrite/read.py", line 157, in read_loom
with connect(filename, 'r', **kwargs) as lc:
File "/opt/venv/lib/python3.7/site-packages/loompy/loompy.py", line 1389, in connect
return LoomConnection(filename, mode, validate=validate)
File "/opt/venv/lib/python3.7/site-packages/loompy/loompy.py", line 82, in init
raise ValueError("\n".join(lv.errors) + f"\n{filename} does not appead to be a valid Loom file according to Loom spec version '{lv.version}'")
...
**Solution**
Simply adding validate=False in https://github.com/vib-singlecell-nf/vsn-pipelines/blob/master/src/utils/bin/sc_file_converter.py on line 257 (as parameter scanpy.read_loom) solves this.
Describe the bug When using a loom file as input, if the loom file has been generated from ScopeLoomR the pipeline crashes.
To Reproduce Steps to reproduce the behavior:
Configure with these options:
Run using this entry point:
See error:
Caused by: Process
single_sample_scenic:SINGLE_SAMPLE:SC__FILE_CONVERTER (1)
terminated with an error exit status (1)Command executed:
/user/leuven/313/vsc31305/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/src/utils/bin/sc_file_converter.py --sample-id "ScoMAP_RNA_VE" --make-var-index-unique false --tag-cell-with-sample-id tr ue --input-format loom --output-format h5ad ScoMAP_RNA_VE.loom "ScoMAP_RNA_VE.SC__FILE_CONVERTER.h5ad"
Command exit status: 1
Command output: (empty)
Command error: Traceback (most recent call last): File "/user/leuven/313/vsc31305/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/src/utils/bin/sc_file_converter.py", line 256, in
sparse=False
File "/opt/venv/lib/python3.7/site-packages/anndata/readwrite/read.py", line 157, in read_loom
with connect(filename, 'r', **kwargs) as lc:
File "/opt/venv/lib/python3.7/site-packages/loompy/loompy.py", line 1389, in connect
return LoomConnection(filename, mode, validate=validate)
File "/opt/venv/lib/python3.7/site-packages/loompy/loompy.py", line 82, in init
raise ValueError("\n".join(lv.errors) + f"\n{filename} does not appead to be a valid Loom file according to Loom spec version '{lv.version}'")
...