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spacemake's Issues
Replace Bio.pairwise2 with Bio.Align.PairwiseAligner
Deprecation warning:
/lib/python3.10/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython.
As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
Reverse R1 mode
It'd be nice to have this separate, for projects where you actually don't need to reverse R1 to match barcodes later on. Can go as an extra var in the modes
error when using mesh_type 'circle'
Using a run_mode with mesh_type: circle always throws the following error:
Error in rule create_mesh_spatial_dge:
jobid: 0
output: projects/slide_seq/processed_data/mouse_brain_v2_meshed/illumina/complete_data/dge/dge.all.polyA_adapter_trimmed.mm_included.spatial_beads.mesh_55_100_Puck_190926_03_bead_loca
tions.h5ad, projects/slide_seq/processed_data/mouse_brain_v2_meshed/illumina/complete_data/dge/dge.all.polyA_adapter_trimmed.mm_included.spatial_beads.mesh_55_100_Puck_190926_03_bead_loca
tions.obs.csv RuleException:
IndexError in line 462 of /data/local/rajewsky/home/lstreng/spacemake_dir_test/spacemake/spacemake/snakemake/main.smk:
index 31353 is out of bounds for axis 0 with size 8896 File "/data/rajewsky/home/lstreng/miniconda_new/envs/spacemake_new/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 2330, in run_wrapper
File "/data/local/rajewsky/home/lstreng/spacemake_dir_test/spacemake/spacemake/snakemake/main.smk", line 462, in __rule_create_mesh_spatial_dge
File "/data/local/rajewsky/home/lstreng/spacemake_dir_test/spacemake/spacemake/spatial/util.py", line 529, in create_meshed_adata
File "/data/local/rajewsky/home/lstreng/spacemake_dir_test/spacemake/spacemake/spatial/util.py", line 339, in aggregate_adata_by_indices File "/data/rajewsky/home/lstreng/miniconda_new/envs/spacemake_new/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 569, in _callback
File "/data/rajewsky/home/lstreng/miniconda_new/envs/spacemake_new/lib/python3.10/concurrent/futures/thread.py", line 58, in run
File "/data/rajewsky/home/lstreng/miniconda_new/envs/spacemake_new/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 555, in cached_or_run
File "/data/rajewsky/home/lstreng/miniconda_new/envs/spacemake_new/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 2362, in run_wrapper
Exiting because a job execution failed. Look above for error message
It happens for all kinds of datasets I have tried (slideseq, visium, stereoseq, ...). It's just the meshing that fails (and things that are dependent on it), everything else works as it should.
Using mesh_type: hexagon on the same data works.
Version is 0.7.1
Add example in the add_barcode_flavor
to showcase how the user has to type the structure, e.g. r1[0:12] etc
Potential bug: some log files have 0 size
Example:
4937 Dec 5 11:24 cutadapt.log
991 Dec 5 11:08 fastq_to_uBAM.log
0 Dec 5 13:53 genome.STAR.bamstats.log
0 Dec 5 13:53 not_genome.STAR.bamstats.log
0 Dec 5 14:13 not_rRNA.bowtie2.bamstats.log
0 Dec 6 09:23 overview_plot.log
0 Dec 5 13:55 rRNA.bowtie2.bamstats.log
221 Dec 5 11:48 rRNA.bowtie2.log
0 Dec 5 13:53 unaligned_bc_tagged.bamstats.log
Replace frame.append with pandas.concat [deprecation warning]
/lib/python3.10/site-packages/spacemake/snakemake/main.smk:770: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
Automatic analysis still fails sometimes
Probably related to a broken ggplot part, but maybe not. Either repair or migrate plots to Python.
Update_sample requires species parameter
After some commit the update_sample command now requires the --species parameter to run, otherwise throws an error, even if the species is already defined for the sample.
regression: can not delete species/reference through cmdline since 0.7 introduced multiple references
spacemake config delete_species --name NAME --reference REF does not work. Instead of deleting only the designated REF it complains that --reference is not a valid argument.
That is at least slightly better than deleting the entire species entry...
Errors when adding barcode_flavor & puck (v0.7.2)
Adding a barcode_flavor or a puck through the command line throws errors:
spacemake config add_barcode_flavor --name NAME --umi r1[10:15] --cell_barcode r1[1:9]
returns
Traceback (most recent call last):
File "/miniconda3/envs/spacemake/bin/spacemake", line 8, in <module>
sys.exit(cmdline())
File "/miniconda3/envs/spacemake/lib/python3.10/site-packages/spacemake/smk.py", line 613, in cmdline
func(args)
File "/miniconda3/envs/spacemake/lib/python3.10/site-packages/spacemake/config.py", line 261, in <lambda>
func = lambda args: add_update_delete_variable_cmdline(config, args)
File "/miniconda3/envs/spacemake/lib/python3.10/contextlib.py", line 79, in inner
return func(*args, **kwds)
File "/miniconda3/envs/spacemake/lib/python3.10/site-packages/spacemake/config.py", line 331, in add_update_delete_variable_cmdline
var_variables = func(variable, name, **args)
File "/miniconda3/envs/spacemake/lib/python3.10/site-packages/spacemake/config.py", line 757, in add_variable
values = self.process_variable_args(variable, **kwargs)
File "/miniconda3/envs/spacemake/lib/python3.10/site-packages/spacemake/config.py", line 722, in process_variable_args
return self.process_barcode_flavor_args(**kwargs)
TypeError: ConfigFile.process_barcode_flavor_args() got an unexpected keyword argument 'name'
And similarly for the puck.
spacemake init --download_species return KeyError
This is the conda list results:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
aioeasywebdav 2.4.0 py39hf3d152e_1001 conda-forge
aiohttp 3.8.1 py39h3811e60_0 conda-forge
aiosignal 1.2.0 pyhd8ed1ab_0 conda-forge
alabaster 0.7.12 pypi_0 pypi
alsa-lib 1.1.5 h516909a_1002 conda-forge
amply 0.1.4 py_0 conda-forge
anndata 0.8.0 pypi_0 pypi
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
asciitree 0.3.3 pypi_0 pypi
async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge
atk-1.0 2.36.0 h3371d22_4 conda-forge
attmap 0.13.2 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pypi_0 pypi
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bcl2fastq2 2.20.0.422 2 bih-cubi
bcrypt 3.2.0 py39h3811e60_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_7 conda-forge
biopython 1.79 pypi_0 pypi
blas 1.0 openblas
boto3 1.21.21 pyhd8ed1ab_0 conda-forge
botocore 1.24.21 pyhd8ed1ab_0 conda-forge
bowtie2 2.4.5 py39hd2f7db1_2 bioconda
brotli 1.0.9 h7f98852_6 conda-forge
brotli-bin 1.0.9 h7f98852_6 conda-forge
brotlipy 0.7.0 py39h3811e60_1003 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.2.1 h06a4308_0
cachetools 5.0.0 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 ha12eb4b_1010 conda-forge
certifi 2021.10.8 py39h06a4308_2
cffi 1.15.0 py39h4bc2ebd_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
cloudpickle 2.0.0 pypi_0 pypi
coin-or-cbc 2.10.7 h3786ebc_0 conda-forge
coin-or-cgl 0.60.3 he7e83c3_2 conda-forge
coin-or-clp 1.17.6 h256e9bb_3 conda-forge
coin-or-osi 0.108.6 h3b589db_2 conda-forge
coin-or-utils 2.11.6 h573740c_0 conda-forge
coincbc 2.10.7 0_metapackage conda-forge
commonmark 0.9.1 pypi_0 pypi
configargparse 1.5.3 pyhd8ed1ab_0 conda-forge
cryptography 36.0.1 py39h95dcef6_0 conda-forge
curl 7.82.0 h7bff187_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dask 2022.2.1 pypi_0 pypi
dask-image 2021.12.0 pypi_0 pypi
datrie 0.8.2 py39h3811e60_3 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
docrep 0.3.2 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
dropbox 11.28.0 pyhd8ed1ab_0 conda-forge
dropseq_tools 2.5.1 hdfd78af_0 bioconda
expat 2.4.7 h27087fc_0 conda-forge
fasteners 0.17.3 pypi_0 pypi
fastqc 0.11.9 hdfd78af_1 bioconda
fftw 3.3.10 nompi_h77c792f_102 conda-forge
filechunkio 1.8 py_2 conda-forge
filelock 3.6.0 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.96 h8e229c2_2 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.30.0 py39hb9d737c_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
frozenlist 1.3.0 py39h3811e60_0 conda-forge
fsspec 2022.2.0 pypi_0 pypi
ftputil 5.0.3 pyhd8ed1ab_0 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_14 conda-forge
gcc_linux-64 9.4.0 h391b98a_7 conda-forge
gdk-pixbuf 2.42.6 h04a7f16_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_14 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_7 conda-forge
ghostscript 9.54.0 h27087fc_2 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gitdb 4.0.9 pyhd8ed1ab_0 conda-forge
gitpython 3.1.27 pyhd8ed1ab_0 conda-forge
google-api-core 2.5.0 pyhd8ed1ab_0 conda-forge
google-api-python-client 2.41.0 pyhd8ed1ab_0 conda-forge
google-auth 2.6.0 pyh6c4a22f_1 conda-forge
google-auth-httplib2 0.1.0 pyhd8ed1ab_0 conda-forge
google-cloud-core 2.2.2 pyh6c4a22f_0 conda-forge
google-cloud-storage 2.1.0 pyh6c4a22f_0 conda-forge
google-crc32c 1.1.2 py39hb81f231_2 conda-forge
google-resumable-media 2.1.0 pyh6c4a22f_0 conda-forge
googleapis-common-protos 1.55.0 py39hf3d152e_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.50.0 h85b4f2f_1 conda-forge
grpcio 1.44.0 py39hff7568b_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gtk2 2.24.33 h539f30e_1 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_14 conda-forge
gxx_linux-64 9.4.0 h0316aca_7 conda-forge
h5py 3.6.0 pypi_0 pypi
harfbuzz 3.4.0 hb4a5f5f_0 conda-forge
htslib 1.15 h9753748_0 bioconda
httplib2 0.20.4 pyhd8ed1ab_0 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
igraph 0.9.9 pypi_0 pypi
imageio 2.16.1 pypi_0 pypi
imagemagick 7.1.0_27 pl5321hae5efcc_0 conda-forge
imagesize 1.3.0 pypi_0 pypi
importlib-metadata 4.11.3 py39hf3d152e_0 conda-forge
importlib_resources 5.4.0 pyhd8ed1ab_0 conda-forge
inflect 5.4.0 pypi_0 pypi
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
java-jdk 8.0.92 1 bioconda
jbig 2.1 h7f98852_2003 conda-forge
jinja2 3.0.3 pyhd8ed1ab_0 conda-forge
jmespath 1.0.0 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pypi_0 pypi
jpeg 9e h7f98852_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.2 py39hf3d152e_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.0 py39hf939315_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
ldc 1.28.1 hcf88599_0 conda-forge
leidenalg 0.8.9 pypi_0 pypi
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h7f98852_6 conda-forge
libbrotlidec 1.0.9 h7f98852_6 conda-forge
libbrotlienc 1.0.9 h7f98852_6 conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 7.82.0 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_14 conda-forge
libgcc-ng 11.2.0 h1d223b6_14 conda-forge
libgd 2.3.3 h283352f_2 conda-forge
libgfortran-ng 11.2.0 h69a702a_14 conda-forge
libgfortran5 11.2.0 h5c6108e_14 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
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libgomp 11.2.0 h1d223b6_14 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
liblapacke 3.9.0 13_linux64_openblas conda-forge
libllvm12 12.0.1 hf817b99_2 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
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libpng 1.6.37 h21135ba_2 conda-forge
libprotobuf 3.19.4 h780b84a_0 conda-forge
librsvg 2.52.5 hc3c00ef_1 conda-forge
libsanitizer 9.4.0 h79bfe98_14 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_14 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_14 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
llvmlite 0.38.0 pypi_0 pypi
locket 0.2.1 pypi_0 pypi
logmuse 0.2.6 pyh8c360ce_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
make 4.3 hd18ef5c_1 conda-forge
markupsafe 2.1.1 py39hb9d737c_0 conda-forge
matplotlib-base 3.5.1 py39h2fa2bec_0 conda-forge
more-itertools 8.12.0 pypi_0 pypi
multidict 6.0.2 py39h3811e60_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.1.0 pypi_0 pypi
nbformat 5.2.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h9c3ff4c_0 conda-forge
networkx 2.7.1 pyhd8ed1ab_0 conda-forge
novosparc 0.4.3 pypi_0 pypi
numba 0.55.1 pypi_0 pypi
numcodecs 0.9.1 pypi_0 pypi
numexpr 2.8.1 pypi_0 pypi
numpy 1.21.5 pypi_0 pypi
numpy-base 1.21.2 py39h2b8c604_0
oauth2client 4.1.3 py_0 conda-forge
omnipath 1.0.5 pypi_0 pypi
openjdk 11.0.1 h600c080_1018 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1m h7f8727e_0
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.1 py39hde0f152_0 conda-forge
pandoc 2.17.1.1 ha770c72_0 conda-forge
pango 1.48.10 h54213e6_2 conda-forge
paramiko 2.10.2 pyhd8ed1ab_0 conda-forge
partd 1.2.0 pypi_0 pypi
patsy 0.5.2 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
peppy 0.31.2 pyhd8ed1ab_2 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.0.1 py39hae2aec6_2 conda-forge
pims 0.5 pypi_0 pypi
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pkg-config 0.29.2 h36c2ea0_1008 conda-forge
pluggy 1.0.0 py39hf3d152e_2 conda-forge
ply 3.11 py_1 conda-forge
pot 0.8.1.0 py39hde0f152_0 conda-forge
prettytable 3.2.0 pyhd8ed1ab_0 conda-forge
protobuf 3.19.4 py39he80948d_0 conda-forge
psutil 5.9.0 py39h3811e60_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulp 2.6.0 py39hf3d152e_0 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pyasn1 0.4.8 py_0 conda-forge
pyasn1-modules 0.2.7 py_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
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pynacl 1.5.0 py39h3811e60_0 conda-forge
pynndescent 0.5.6 pypi_0 pypi
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py39h3811e60_0 conda-forge
pysam 0.18.0 py39h5030a8b_2 bioconda
pysftp 0.2.9 py_1 conda-forge
pysocks 1.7.1 py39hf3d152e_4 conda-forge
pytest 7.1.0 py39hf3d152e_0 conda-forge
python 3.9.10 h85951f9_2_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-irodsclient 1.1.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pywavelets 1.3.0 pypi_0 pypi
pyyaml 6.0 py39h3811e60_3 conda-forge
r-askpass 1.1 r41hcfec24a_2 conda-forge
r-assertthat 0.2.1 r41hc72bb7e_2 conda-forge
r-backports 1.4.1 r41hcfec24a_0 conda-forge
r-base 4.1.2 hde4fec0_0 conda-forge
r-base64enc 0.1_3 r41hcfec24a_1004 conda-forge
r-bit 4.0.4 r41hcfec24a_0 conda-forge
r-bit64 4.0.5 r41hcfec24a_0 conda-forge
r-blob 1.2.2 r41hc72bb7e_0 conda-forge
r-brio 1.1.3 r41hcfec24a_0 conda-forge
r-broom 0.7.12 r41hc72bb7e_0 conda-forge
r-bslib 0.3.1 r41hc72bb7e_0 conda-forge
r-cachem 1.0.6 r41hcfec24a_0 conda-forge
r-callr 3.7.0 r41hc72bb7e_0 conda-forge
r-cellranger 1.1.0 r41hc72bb7e_1004 conda-forge
r-cli 3.2.0 r41h03ef668_0 conda-forge
r-clipr 0.8.0 r41hc72bb7e_0 conda-forge
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r-colorspace 2.0_3 r41h06615bd_0 conda-forge
r-commonmark 1.8.0 r41h06615bd_0 conda-forge
r-cowplot 1.1.1 r41hc72bb7e_0 conda-forge
r-cpp11 0.4.2 r41hc72bb7e_0 conda-forge
r-crayon 1.5.0 r41hc72bb7e_0 conda-forge
r-crosstalk 1.2.0 r41hc72bb7e_0 conda-forge
r-curl 4.3.2 r41hcfec24a_0 conda-forge
r-data.table 1.14.2 r41hcfec24a_0 conda-forge
r-dbi 1.1.2 r41hc72bb7e_0 conda-forge
r-dbplyr 2.1.1 r41hc72bb7e_0 conda-forge
r-desc 1.4.0 r41hc72bb7e_0 conda-forge
r-dichromat 2.0_0 r41ha770c72_2002 conda-forge
r-diffobj 0.3.5 r41hcfec24a_0 conda-forge
r-digest 0.6.29 r41h03ef668_0 conda-forge
r-dplyr 1.0.7 r41h03ef668_0 conda-forge
r-dtplyr 1.2.1 r41hc72bb7e_0 conda-forge
r-ellipsis 0.3.2 r41hcfec24a_0 conda-forge
r-evaluate 0.15 r41hc72bb7e_0 conda-forge
r-fansi 1.0.2 r41hcfec24a_0 conda-forge
r-farver 2.1.0 r41h03ef668_0 conda-forge
r-fastmap 1.1.0 r41h03ef668_0 conda-forge
r-fontawesome 0.2.2 r41hc72bb7e_0 conda-forge
r-forcats 0.5.1 r41hc72bb7e_0 conda-forge
r-fs 1.5.2 r41h03ef668_0 conda-forge
r-gargle 1.2.0 r41hc72bb7e_0 conda-forge
r-gdtools 0.2.4 r41h42e24d8_0 conda-forge
r-generics 0.1.2 r41hc72bb7e_0 conda-forge
r-ggplot2 3.3.5 r41hc72bb7e_0 conda-forge
r-glue 1.6.2 r41h06615bd_0 conda-forge
r-googledrive 2.0.0 r41hc72bb7e_0 conda-forge
r-googlesheets4 1.0.0 r41h785f33e_0 conda-forge
r-gtable 0.3.0 r41hc72bb7e_3 conda-forge
r-haven 2.4.3 r41h2713e49_0 conda-forge
r-hexbin 1.28.2 r41h8da6f51_0 conda-forge
r-highr 0.9 r41hc72bb7e_0 conda-forge
r-hms 1.1.1 r41hc72bb7e_0 conda-forge
r-htmltools 0.5.2 r41h03ef668_0 conda-forge
r-htmlwidgets 1.5.4 r41hc72bb7e_0 conda-forge
r-httpuv 1.6.5 r41h03ef668_0 conda-forge
r-httr 1.4.2 r41hc72bb7e_0 conda-forge
r-ids 1.0.1 r41hc72bb7e_1 conda-forge
r-isoband 0.2.5 r41h03ef668_0 conda-forge
r-jquerylib 0.1.4 r41hc72bb7e_0 conda-forge
r-jsonlite 1.8.0 r41h06615bd_0 conda-forge
r-kableextra 1.3.4 r41hc72bb7e_0 conda-forge
r-knitr 1.37 r41hc72bb7e_1 conda-forge
r-labeling 0.4.2 r41hc72bb7e_1 conda-forge
r-later 1.2.0 r41h03ef668_0 conda-forge
r-lattice 0.20_45 r41hcfec24a_0 conda-forge
r-lazyeval 0.2.2 r41hcfec24a_2 conda-forge
r-lifecycle 1.0.1 r41hc72bb7e_0 conda-forge
r-lubridate 1.8.0 r41h03ef668_0 conda-forge
r-magrittr 2.0.2 r41hcfec24a_0 conda-forge
r-manipulatewidget 0.11.1 r41hc72bb7e_0 conda-forge
r-mapproj 1.2.8 r41hcfec24a_0 conda-forge
r-maps 3.4.0 r41hcfec24a_0 conda-forge
r-mass 7.3_55 r41hcfec24a_0 conda-forge
r-matrix 1.4_0 r41he454529_0 conda-forge
r-mgcv 1.8_39 r41h0154571_0 conda-forge
r-mime 0.12 r41hcfec24a_0 conda-forge
r-miniui 0.1.1.1 r41hc72bb7e_1002 conda-forge
r-modelr 0.1.8 r41hc72bb7e_0 conda-forge
r-munsell 0.5.0 r41hc72bb7e_1004 conda-forge
r-nlme 3.1_155 r41h859d828_0 conda-forge
r-openssl 2.0.0 r41hfaab4ff_0 conda-forge
r-pals 1.7 r41hc72bb7e_0 conda-forge
r-pillar 1.7.0 r41hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r41hc72bb7e_1 conda-forge
r-pkgload 1.2.4 r41h03ef668_0 conda-forge
r-praise 1.0.0 r41hc72bb7e_1005 conda-forge
r-prettyunits 1.1.1 r41hc72bb7e_1 conda-forge
r-processx 3.5.2 r41hcfec24a_0 conda-forge
r-progress 1.2.2 r41hc72bb7e_2 conda-forge
r-promises 1.2.0.1 r41h03ef668_0 conda-forge
r-ps 1.6.0 r41hcfec24a_0 conda-forge
r-purrr 0.3.4 r41hcfec24a_1 conda-forge
r-r6 2.5.1 r41hc72bb7e_0 conda-forge
r-rappdirs 0.3.3 r41hcfec24a_0 conda-forge
r-rcolorbrewer 1.1_2 r41h785f33e_1003 conda-forge
r-rcpp 1.0.8.2 r41h7525677_0 conda-forge
r-readr 2.1.2 r41h03ef668_0 conda-forge
r-readxl 1.3.1 r41h2713e49_4 conda-forge
r-rematch 1.0.1 r41hc72bb7e_1004 conda-forge
r-rematch2 2.1.2 r41hc72bb7e_1 conda-forge
r-reprex 2.0.1 r41hc72bb7e_0 conda-forge
r-rgl 0.108.3 r41hbf98b08_0 conda-forge
r-rlang 0.4.12 r41hcfec24a_0 conda-forge
r-rmarkdown 2.13 r41hc72bb7e_1 conda-forge
r-rprojroot 2.0.2 r41hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r41hc72bb7e_0 conda-forge
r-rvest 1.0.2 r41hc72bb7e_0 conda-forge
r-sass 0.4.0 r41h03ef668_0 conda-forge
r-scales 1.1.1 r41hc72bb7e_0 conda-forge
r-selectr 0.4_2 r41hc72bb7e_1 conda-forge
r-shiny 1.7.1 r41h785f33e_0 conda-forge
r-shinyjs 2.1.0 r41hc72bb7e_0 conda-forge
r-sourcetools 0.1.7 r41h03ef668_1002 conda-forge
r-stringi 1.7.6 r41h337692f_1 conda-forge
r-stringr 1.4.0 r41hc72bb7e_2 conda-forge
r-svglite 2.1.0 r41h03ef668_0 conda-forge
r-sys 3.4 r41hcfec24a_0 conda-forge
r-systemfonts 1.0.4 r41hef9c87a_0 conda-forge
r-testthat 3.1.2 r41h03ef668_0 conda-forge
r-tibble 3.1.6 r41hcfec24a_0 conda-forge
r-tidyr 1.2.0 r41h03ef668_0 conda-forge
r-tidyselect 1.1.1 r41hc72bb7e_0 conda-forge
r-tidyverse 1.3.1 r41hc72bb7e_0 conda-forge
r-tinytex 0.37 r41hc72bb7e_0 conda-forge
r-tzdb 0.2.0 r41h03ef668_0 conda-forge
r-utf8 1.2.2 r41hcfec24a_0 conda-forge
r-uuid 1.0_4 r41h06615bd_0 conda-forge
r-vctrs 0.3.8 r41hcfec24a_1 conda-forge
r-viridislite 0.4.0 r41hc72bb7e_0 conda-forge
r-vroom 1.5.7 r41h03ef668_0 conda-forge
r-waldo 0.3.1 r41hc72bb7e_0 conda-forge
r-webshot 0.5.2 r41hc72bb7e_1 conda-forge
r-withr 2.5.0 r41hc72bb7e_0 conda-forge
r-xfun 0.30 r41h7525677_0 conda-forge
r-xml2 1.3.3 r41h03ef668_0 conda-forge
r-xtable 1.8_4 r41hc72bb7e_3 conda-forge
r-yaml 2.3.5 r41h06615bd_0 conda-forge
ratelimiter 1.2.0 py_1002 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
recommonmark 0.7.1 pypi_0 pypi
requests 2.27.1 pyhd8ed1ab_0 conda-forge
rsa 4.8 pyhd8ed1ab_0 conda-forge
s3transfer 0.5.2 pyhd8ed1ab_0 conda-forge
sambamba 0.8.2 h98b6b92_2 bioconda
samtools 1.15 h1170115_1 bioconda
scanpy 1.8.2 pypi_0 pypi
scikit-image 0.19.2 pypi_0 pypi
scikit-learn 1.0.2 pypi_0 pypi
scikit-misc 0.1.4 pypi_0 pypi
scipy 1.8.0 py39hee8e79c_1 conda-forge
seaborn 0.11.2 pypi_0 pypi
sed 4.8 he412f7d_0 conda-forge
setuptools 60.10.0 py39hf3d152e_0 conda-forge
sinfo 0.3.4 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
slacker 0.14.0 py_0 conda-forge
slicerator 1.0.0 pypi_0 pypi
smart_open 5.2.1 pyhd8ed1ab_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snakemake 6.3.0 hdfd78af_0 bioconda
snakemake-minimal 6.3.0 pyhdfd78af_0 bioconda
snowballstemmer 2.2.0 pypi_0 pypi
spacemake 0.4.3 pypi_0 pypi
sphinx 4.4.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlite 3.37.1 h4ff8645_0 conda-forge
squidpy 1.1.2 pypi_0 pypi
star 2.7.10a h9ee0642_0 bioconda
statsmodels 0.13.2 pypi_0 pypi
stdlib-list 0.8.0 pypi_0 pypi
stone 3.3.1 pyhd8ed1ab_0 conda-forge
stopit 1.1.2 py_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tables 3.7.0 pypi_0 pypi
tbb 2020.2 h4bd325d_4 conda-forge
texttable 1.6.4 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tifffile 2022.3.16 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.11.2 pypi_0 pypi
toposort 1.7 pyhd8ed1ab_0 conda-forge
tqdm 4.63.0 pypi_0 pypi
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.1.1 hd8ed1ab_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
ubiquerg 0.6.1 pyh9f0ad1d_0 conda-forge
umap-learn 0.5.2 pypi_0 pypi
unicodedata2 14.0.0 py39h3811e60_0 conda-forge
uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
veracitools 0.1.3 py_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.14.0 py39hb9d737c_0 conda-forge
xarray 2022.3.0 pypi_0 pypi
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.7.2 py39h3811e60_1 conda-forge
zarr 2.11.1 pypi_0 pypi
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
Catch errors in the sample sheet
If the sample sheet is compromised or doesn't have the appropriate info, throw informative messages for the user to check.
Reduce number of threads in fastq -> BAM
Rule in the drop-dropseq branch gives up to 32 threads, but most are not used because of I/O being the bottleneck.
Benchmark I/O vs # of different samples and select a better value.
Samples merging is broken after updating map_strategy
Inherit sample attributes when merging samples
When spacemake projects merge merge the common attributes (investigator, species -- important otherwise pipeline cannot run, etc).
spacemake projects merge_samples
It seems that it currently starts from merging .fastq files. Is it not better to start much downstream of that, from the bam files?
loading the STAR mapping index takes long. Treat this as a service
snakemake support 'services' https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#service-rules-jobs
which can be started and stopped. Sounds like a perfect fit for loading the STAR genome index and releasing it again after the last instance has quit. In the meantime, STAR mapping jobs do not have to load their own copy of the genome index which would make them faster to start mappting and reduce overall memory footprint
Fixing the header problem when mapping
STAR omits some info from the header and some Picard tools complain about it. Current workaround uses a python script which takes quite some time to rewrite the bam file.
A quicker solution that fixes the problem is to explicitly add the header values when mapping with star as:
--outSAMattrRGline ID:A SM:${name}
${name} needs to be the same with the filename produced upstream. Not sure how universal ID:A is, please check for consistency.
Fix issue when deleting sample
Tryting spacemake projects delete_sample --project_id project --sample_id sample throws a KeyError: KeyError: 'project_id_list'
config set_run_mode bug
Throws an error of the type
msg += f'SUCCESS: run mode: {run_mode} {action_msg} succesfully.\n'
NameError: name 'run_mode' is not defined
restore cmd line functionality for adding barcode_flavor
Functionality is currently broken on the master branch.
spacemake config add_barcode_flavor
usage: spacemake config add_barcode_flavor [-h] --name NAME --umi UMI --cell_barcode CELL_BARCODE
spacemake config add_barcode_flavor: error: the following arguments are required: --name, --umi, --cell_barcode
Giving name, umi and cell_barcode does not work:
spacemake config add_barcode_flavor --name fc_sts_miniseq --umi r2[0:9] --cell_barcode r1[2:27]
add_variable() called with variable=barcode_flavors name=fc_sts_miniseq kw={'umi': 'r2[0:9]', 'cell_barcode': 'r1[2:27]', 'name': 'fc_sts_miniseq'}
Traceback (most recent call last):
File "../miniconda3/envs/smk/bin/spacemake", line 8, in <module>
sys.exit(cmdline())
File "../miniconda3/envs/smk/lib/python3.10/site-packages/spacemake/smk.py", line 604, in cmdline
func(args)
File "../miniconda3/envs/smk/lib/python3.10/site-packages/spacemake/config.py", line 261, in <lambda>
func = lambda args: add_update_delete_variable_cmdline(config, args)
File "../miniconda3/envs/smk/lib/python3.10/contextlib.py", line 79, in inner
return func(*args, **kwds)
File "../miniconda3/envs/smk/lib/python3.10/site-packages/spacemake/config.py", line 331, in add_update_delete_variable_cmdline
var_variables = func(variable, name, **args)
File "../miniconda3/envs/smk/lib/python3.10/site-packages/spacemake/config.py", line 745, in add_variable
values = self.process_variable_args(variable, **kwargs)
File "../miniconda3/envs/smk/lib/python3.10/site-packages/spacemake/config.py", line 710, in process_variable_args
return self.process_barcode_flavor_args(**kwargs)
TypeError: ConfigFile.process_barcode_flavor_args() got an unexpected keyword argument 'name'
List of small stuff before freezing paper release
- Ship
run_modeandbarcode_flavor - Ship
puck - Ship second
flowcell_coordinate_system.csv - Double-check the adapter
Change join from `inner` to `outer` when stitching pucks
Just so that we don't forget. It currently results in decreased number of genes.
Error "version" with spacemake config add_species
Hi ! After downloading human data, I try to launch spacemake config add_species with the following command :
spacemake config add_species --name human --genome PATH/species_data/human/GRCh38.primary_assembly.genome.fa.gz --annotation PATH/species_data/human/gencode.v38.primary_assembly.annotation.gtf.gz
but I have the error :
Traceback (most recent call last):
File "/home/user/anaconda3/envs/spacemake/bin/spacemake", line 8, in
sys.exit(cmdline())
File "/home/user/anaconda3/envs/spacemake/lib/python3.9/site-packages/spacemake/smk.py", line 611, in cmdline
func(args)
File "/home/user/anaconda3/envs/spacemake/lib/python3.9/site-packages/spacemake/config.py", line 234, in
func = lambda args: add_update_delete_variable_cmdline(config, args)
File "/home/user/anaconda3/envs/spacemake/lib/python3.9/contextlib.py", line 79, in inner
return func(*args, **kwds)
File "/home/user/anaconda3/envs/spacemake/lib/python3.9/site-packages/spacemake/config.py", line 305, in add_update_delete_variable_cmdline
var_variables = func(variable, name, **args)
File "/home/user/anaconda3/envs/spacemake/lib/python3.9/site-packages/spacemake/config.py", line 661, in add_variable
values = self.process_variable_args(variable, **kwargs)
File "/home/user/anaconda3/envs/spacemake/lib/python3.9/site-packages/spacemake/config.py", line 655, in process_variable_args
return self.process_species_args(**kwargs)
TypeError: process_species_args() got an unexpected keyword argument 'version'
Do you know this problem, and if yes, can you please help me to overcome it ? Thanks in advance for your answer !
Enable parallelism of DGE creation for multiple pucks
There's currently a for chunk that iterates over all pucks, one by one. Enable parallelism for that -- can be potentially solved directly in the quant.py.
Minor bug in spacemake merge
Seems like the flag samtools merge -O is currently set to samtools merge -o so that it crashes.
Error when adding the --download_species during init
Starting with a fresh installation (v0.7.2), adding the --download_species during initialization
spacemake init --download_species human --dropseq_tools /Drop-seq_tools-2.5.1/
throws an error:
usage: spacemake [-h] [--version] {init} ...
spacemake: error: unrecognized arguments: human
config add_run_mode
- Shall we not change the
spacemake config add_run_modeto have Boolean vars instead of e.g.clean_dgeandno-clean_dge? If you doconfig list_modesthey anyway appear Boolean. - Creating a new mode with
--plot_bead_size 1creates a mode which after listing it showsplot_bead_size: '1'. Hints that it saves it as string and not asintorfloat
add/update_sample needs to validate --map_strategy
Currently, no validation of the map_strategy string is performed when adding or updating a sample. If a reference is used that does not exist in the config.yaml, this triggers a confusing KeyError in mapping.smk during spacemake run.
Expected behavior: An exception should be thrown when adding or updating a sample with an invalid map_strategy.
Missing input files for rule symlinks
Hi, I'm trying to launch run of spacemake
I've installed everything and bump into two errors:
first. spacemake init --dropseq_tools /home/eugenea/bin/Drop-seq_tools-2.5.1 --download_species human --download_species
finishes snakemake part, but seems to fails later
Second. (after re-init with the downloaded genomes spacemake config add_species --name homo_sapiens --reference genome --sequence /home/eugenea/spacemake_test/species_data/human/human_genome.fa --annotation /home/eugenea/spacemake_test/species_data/human/human_annotation.gtf ) Spacemake fails to build dag
project was added like in the docs:
spacemake projects add_sample \
--project_id spacemake_test_run \
--sample_id visq_test \
--R1 /home/data/fastq/100086/scRNAseq/vis1_S1_L001_R1_001.fastq.gz /home/data/fastq/100086/scRNAseq/vis1_S1_L002_R1_001.fastq.gz \
--R2 /home/data/fastq/100086/scRNAseq/vis1_S1_L001_R2_001.fastq.gz /home/data/fastq/100086/scRNAseq/vis1_S1_L002_R2_001.fastq.gz \
--species homo_sapiens \
--puck visium \
--run_mode visium \
--barcode_flavor visium
Best, Eugene
QC_sheet rRNA % is wrong
It's currently computed from the STAR input reads and not from the total reads as it should.
(Eventually migrate to python qc sheets anyway)
spatial barcodes are not processed during downsampling
When running spacemake run downsample on a dataset with spatial pucks, the output at the different downsampling levels only generates the dge files for the _beads_no_spatial_data, and for none of the spatial pucks specified for the sample.
This issue was observed in 0.5.5 and 0.7.2 (potentially on other versions, too)
Minor suggestions v2
- Consider keeping only
trueandfalse(i.e. remove capital letters) to clean the clutter - Consider offering a
seqscopeand anscRNAseqrun mode with sensible defaults - In the
barcode_flavorswe need doumentation / example for theadd_barcode_flavor. Ther1[x:y]structure is not clear to a new user. Also need to explain the numbering, i.e. that 0 is the first base and the second number is not inclusive - i still think
spacemake projects listshould also list barcode flavor and run modes - offer the user the option to use an existing genome index
- where exactly do we define the rRNA index? Starting from scratch I don't see it anywhere and hence usually skip it
'barcodes' variable of 'pucks' not recognised, spacemake thinks sample is not spatial
sample is only spatial right now if puck_barcode_file specifically provided
when puck has barcodes it fails to use it
Samples merging seems to write in the original directories
barcode flavor not updating
Seems like set_barcode_flavor doesn't update the flavor for the sample?
Unify flags in cmd-line
Some of the commands require flags, others don't. Example:
spacemake projects set_barcode_flavor --project_id etc
but
spacemake config add_barcode_flavor --name name
doesn't work currently
List of joined spatial units in meshed adata
In the function
spacemake/spacemake/spatial/util.py
Lines 273 to 281 in 3502946
The "meshed" adata_out object constitutes the main output, e.g.,
spacemake/spacemake/spatial/util.py
Lines 419 to 422 in 3502946
For some analyses, it is relevant to have a list of spatial units that have been merged into each newly created mesh cell. That is, for each new cell in adata_out, a list of spots. This can be done by index (pointing to the .obs_names in the adata input), such that it can be stored as a sparse matrix where 1 denotes mapping.
I propose both of these lists can be stored as adata_out.uns["indices_joined_spatial_units"] and adata_out.uns["spatial_units_obs_names"]. The purpose of this second list is to keep track of the adata.obs_names, which could contain relevant information such as cell barcodes that can be traced back to the final bam file.
Edit 1:
It is important to modularize spacemake.spatial.util.create_meshed_adata by separating the mapping of spatial units to the mesh and the construction of the adata. This is helpful when integrating other types of spatial unit aggregation (e.g., supported by segmentation).
Fix demux dependency on drop-dropseq branch
MissingInputException when merging with 0.7.2
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:
Add support for updating R1/R2 in update_sample function
There's currently no functionality for that:
$ spacemake projects update_sample
usage: spacemake projects update_sample [-h] --project_id PROJECT_ID --sample_id SAMPLE_ID [--barcode_flavor BARCODE_FLAVOR] [--adapter_flavor ADAPTER_FLAVOR] [--species SPECIES]
[--map_strategy MAP_STRATEGY] [--puck PUCK] [--puck_barcode_file_id PUCK_BARCODE_FILE_ID [PUCK_BARCODE_FILE_ID ...]]
[--puck_barcode_file PUCK_BARCODE_FILE [PUCK_BARCODE_FILE ...]] [--run_mode RUN_MODE [RUN_MODE ...]] [--investigator INVESTIGATOR] [--experiment EXPERIMENT]
[--sequencing_date SEQUENCING_DATE]
Possible error that produces empty panels in the qc_sheet
Change default mapping strategy
Change bowtie2:rRNA,STAR:genome:final to bowtie2:rRNA->STAR:genome:final
project_id should encompass sample_id
Attempting to change the species from mouse to human for all samples within a project doesn't work.
spacemake projects update_sample --project_id SP115 --species human gives an error
spacemake projects update_sample: error: the following arguments are required: --sample_id
Since project_id contains all sample_ids, do we want to go ahead with the change without specifying sample_ids?
Ship `openst` barcode_flavor and run_mode with spacemake
Minor improvements / additions / corrections
Several thoughts and minor stuff to consider:
- Can we give the user the option NOT to index but to import an indexed genome?
-
spacemake config add_run_modecurrently returns an error instead of listing the variables. - Same with
spacemake config update_run_mode -
spacemake projects set_run_modekeeps the default inside. Why do we need that? Maybe if the user sets the mode remove the default? removing it withremove_run_modeworks fine though. - In the statements
(average 106608.958 reads/second). Just round and remove the decimals to reduce clutter. Same where we report time. - During mapping there's an error
[E::idx_find_and_load] Could not retrieve index file for '/dev/stdin'. Is this any problem? - Shall we not have
STARverbose and see the mapping progress? Right now we only report the gene tagging. -
spacemake projects merge_samplesdoesn't inheritbarcode_flavor(spacemake v.0.0.2) -
samtools mergehas a@flag for multi-threading. We should totally use that. - When merging starts, print a line saying something like
merging sample1 and sample2 - Sambamba throws an error
sambamba: error while loading shared libraries: libphobos2-ldc-shared.so.81: cannot open shared object file: No such file or directorybut doesn't seem to affect.
Restrict number of threads for create_spatial_barcode
This seems to be a snakemake issue that results in spacemake crashing when >15 threads are used.
Cannot run spacemake after updating run_mode
After deleting the projects directory and even the species, spacemake refuses to run. (projects list and config run fine giving the expected output). Below the error
$ spacemake run --cores 30
Building DAG of jobs...
WorkflowError in line 64 of .../lib/python3.9/site-packages/spacemake/snakemake/dropseq.smk:
Function did not return str or list of str.
Fix add_barcode_flavor issues
- if
sample_idis missing, by default it adds the flavor to all samples in the project. The message should list the sample_ids that have changed, currently it saysand for samples: [''] - if random names are inputted, it doesn't throw an error but instead returns a normal message like
Setting barcode flavor: scrnaseq for projects: ['KO'] and for samples: ['this_shouldnt_run']
--------------------------------------------------
SUCCESS: barcode_flavor set successfully.
Support for FFPE?
Hi, Thank you for making this user-friendly package. I am wondering if there is support for Visium FFPE data coming? Thanks.
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