kfukuta/wf-transcriptomes-v202
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Fix overwritten DGE results file

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This commit is contained in:
Neil Horner 2025-02-18 17:05:45 +00:00
parent 91a514abd2
commit b62722751f
3 changed files with 3 additions and 3 deletions
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2
CHANGELOG.md
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@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `split_bam` and `build_minimap_index_transcriptome` process memory allocation increased. - `split_bam` and `build_minimap_index_transcriptome` process memory allocation increased.
- Updated recommended memory requirement. - Updated recommended memory requirement.
- Updated project description. - Updated project description.
### Fixed
- `all_gene_counts.tsv` contained the DE counts results.
## [v1.6.1] ## [v1.6.1]
### Fixed ### Fixed

3
bin/workflow_glue/de_plots.py
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@ -276,13 +276,12 @@ def de_section(
lambda x: gid_to_gene_name.get(x))) lambda x: gid_to_gene_name.get(x)))
df_dge.to_csv('results_dge.tsv', index=True, index_label="gene_id", sep="\t") df_dge.to_csv('results_dge.tsv', index=True, index_label="gene_id", sep="\t")
# write_dge(gene_counts, gid_to_gene_name, "all_gene_counts.tsv")
df_gene_counts = pd.read_csv(gene_counts, sep='\t') df_gene_counts = pd.read_csv(gene_counts, sep='\t')
df_gene_counts.insert( df_gene_counts.insert(
0, 'gene_name', df_gene_counts.index.map( 0, 'gene_name', df_gene_counts.index.map(
lambda x: gid_to_gene_name.get(x))) lambda x: gid_to_gene_name.get(x)))
df_gene_counts.to_csv( df_gene_counts.to_csv(
'results_dge.tsv', index=True, index_label="gene_id", sep="\t") 'all_gene_counts.tsv', index=True, index_label="gene_id", sep="\t")
df_filtered = pd.read_csv(filtered, sep='\t') df_filtered = pd.read_csv(filtered, sep='\t')
df_filtered.insert(1, "gene_name", df_filtered.gene_id.map( df_filtered.insert(1, "gene_name", df_filtered.gene_id.map(

1
main.nf
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@ -25,7 +25,6 @@ process getVersions {
script: script:
""" """
python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
python -c "import aplanat; print(f'aplanat,{aplanat.__version__}')" >> versions.txt
python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
fastcat --version | sed 's/^/fastcat,/' >> versions.txt fastcat --version | sed 's/^/fastcat,/' >> versions.txt