Fix overwritten DGE results file

CHANGELOG.md

@@ -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.
 - Updated recommended memory requirement.
 - Updated project description.
+### Fixed
+- `all_gene_counts.tsv` contained the DE counts results.
 
 ## [v1.6.1]
 ### Fixed

bin/workflow_glue/de_plots.py

@@ -276,13 +276,12 @@ def de_section(
             lambda x: gid_to_gene_name.get(x)))
         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.insert(
             0, 'gene_name', df_gene_counts.index.map(
                 lambda x: gid_to_gene_name.get(x)))
         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.insert(1, "gene_name", df_filtered.gene_id.map(

main.nf

@@ -25,7 +25,6 @@ process getVersions {
     script:
     """
     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 sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
     fastcat --version | sed 's/^/fastcat,/' >> versions.txt