Standardize conversion workflow #65
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Nov 29, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
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github-actions / JUnit Test Report
nf.test-dataset_cellrangermulti_aligner
Assertion failed:
25 of 27 assertions failed
Raw output
Nextflow stdout:
ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (4PLEX_HUMAN)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (4PLEX_HUMAN)` terminated with an error exit status (1)
Command executed [/home/runner/work/scrnaseq/scrnaseq/./workflows/../modules/local/templates/mtx_to_h5ad_cellranger.py]:
#!/usr/bin/env python
# Set numba chache dir to current working directory (which is a writable mount also in containers)
import os
os.environ["NUMBA_CACHE_DIR"] = "."
import scanpy as sc
import pandas as pd
import argparse
import anndata
from anndata import AnnData
import platform
def _mtx_to_adata(
input: str,
sample: str,
):
adata = sc.read_10x_h5(input)
adata.var["gene_symbols"] = adata.var_names
adata.var.set_index("gene_ids", inplace=True)
adata.obs["sample"] = sample
# reorder columns for 10x mtx files
adata.var = adata.var[["gene_symbols", "feature_types", "genome"]]
return adata
def format_yaml_like(data: dict, indent: int = 0) -> str:
"""Formats a dictionary to a YAML-like string.
Args:
data (dict): The dictionary to format.
indent (int): The current indentation level.
Returns:
str: A string formatted as YAML.
"""
yaml_str = ""
for key, value in data.items():
spaces = " " * indent
if isinstance(value, dict):
yaml_str += f"{spaces}{key}:\n{format_yaml_like(value, indent + 1)}"
else:
yaml_str += f"{spaces}{key}: {value}\n"
return yaml_str
def dump_versions():
versions = {
"NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD": {
"python": platform.python_version(),
"scanpy": sc.__version__,
"pandas": pd.__version__,
"anndata": anndata.__version__,
}
}
with open("versions.yml", "w") as f:
f.write(format_yaml_like(versions))
def input_to_adata(
input_data: str,
output: str,
sample: str,
):
print(f"Reading in {input_data}")
# open main data
adata = _mtx_to_adata(input_data, sample)
# standard format
# index are gene IDs and symbols are a column
adata.var['gene_versions'] = adata.var.index
adata.var.index = adata.var['gene_versions'].str.split('.').str[0].values
adata.var_names_make_unique()
# write results
adata.write_h5ad(f"{output}")
print(f"Wrote h5ad file to {output}")
# dump versions
dump_versions()
return adata
#
# Run main script
#
# create the directory with the sample name
os.makedirs("4PLEX_HUMAN", exist_ok=True)
# input_type comes from NF module
adata = input_to_adata(
input_data="null_feature_bc_matrix.h5",
output="4PLEX_HUMAN_null_matrix.h5ad",
sample="4PLEX_HUMAN"
)
Command exit status:
1
Command output:
Reading in null_feature_bc_matrix.h5
Command error:
6360b3717211: Pull complete
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6f63df1cb8dd: Verifying Checksum
6f63df1cb8dd: Download complete
53269d96152a: Verifying Checksum
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ba94160d36b7: Verifying Checksum
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c864db06f68b: Pull complete
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53269d96152a: Pull complete
54ba407d13f5: Verifying Checksum
54ba407d13f5: Download complete
54ba407d13f5: Pull complete
Digest: sha256:fbd40d3d00751ac0df11564b3697006ecf8604af48960833910d32755033575f
Status: Downloaded newer image for community.wave.seqera.io/library/scanpy:1.10.2--e83da2205b92a538
Reading in null_feature_bc_matrix.h5
Traceback (most recent call last):
File ".command.sh", line 94, in <module>
adata = input_to_adata(
^^^^^^^^^^^^^^^
File ".command.sh", line 69, in input_to_adata
adata = _mtx_to_adata(input_data, sample)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".command.sh", line 20, in _mtx_to_adata
adata = sc.read_10x_h5(input)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/legacy_api_wrap/__init__.py", line 80, in fn_compatible
return fn(*args_all, **kw)
^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/scanpy/readwrite.py", line 203, in read_10x_h5
with h5py.File(str(filename), "r") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/h5py/_hl/files.py", line 562, in __init__
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/h5py/_hl/files.py", line 235, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 102, in h5py.h5f.open
FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = 'null_feature_bc_matrix.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
Work dir:
/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/c7d364337517d05e62c09dbb6cb11b88/work/c3/033f7ab6a792ea6c2d64c0f651efb3
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/c7d364337517d05e62c09dbb6cb11b88/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/c7d364337517d05e62c09dbb6cb11b88/meta/nextflow.log' file for details
Nextflow stderr:
Nextflow 24.10.2 is available - Please consider updating your version to it
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