burtonjake
commented
1 month ago All the libraries used across the current MR. PARETO Snakefiles:
unsupervised_analysis
import os
import sys
import pandas as pd
import yaml
from snakemake.utils import min_version
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spilterlize_integrate
import yaml
import pandas as pd
import os
from snakemake.utils import validate, min_version
import json
import csv
import sys
import subprocess
---
dea_limma
import os
import sys
import pandas as pd
import yaml
from snakemake.utils import min_version
---
enrichment_analysis
import yaml
import pandas as pd
import os
from snakemake.utils import validate, min_version
import json
import csv
import sys
import subprocess
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genome_tracks
# libraries
import pandas as pd
import os
import gzip
import re # for regular expressions
import numpy as np
import json
from snakemake.utils import min_version
import hashlib # generating unique sample names for single-cell samples
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atacseq_pipeline
import yaml
import pandas as pd
import os
import shutil
from snakemake.utils import validate, min_version
from string import Template
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scrnaseq_processing_seurat
import os
import sys
import pandas as pd
import yaml
from snakemake.utils import min_version
---
dea_seurat
import os
import sys
import pandas as pd
import yaml
from snakemake.utils import min_version
---
mixscape_seurat
import os
import sys
import pandas as pd
import yaml
from snakemake.utils import min_versionIt seems like the only one's that are not from the Python Standard Library are pandas, numpy and pyyaml. We should at least document the numpy and pandas dependencies.
sreichl
To bump all modules to snakemake 8 (#12) we primarily need to document the libraries required to process the initial Snakemake file. These should be added to
envs/global.yamland cross-linked into the Snakemake file with acondadirective. See 'global workflow dependencies' in the snakemake docs. We also need to check the documentation for each module such that it makes sense for Snakemake8.one-off (first in unsupervised_analysis)
envs/global.yamlspecifying required software for Snakefile executionconfig.yamlfor each module
partitionparameter fromparamsworkflow/profiles/default/config.yamlenvs/global.yamlto workflowconfig/README.mdcondadirective inSnakefilefor global specifications at the beginning of your workflow, before you import or use any of those additional packages8.20.1Modules