[BUG] Pipeline crashing when starting from SCopeLoomR loom files

[cbravo93]

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:

1. 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

2. 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

3. 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 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 <module>
      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.

[cflerin]

@cbravo93 , you can try the fix in the develop branch