Fix linting

CITATIONS.md

@@ -101,4 +101,4 @@
 
 - [Meslier (2022)](https://doi.org/10.1038/s41597-022-01762-z) (AWS Full Test data)
 
-  > Meslier, Victoria, Benoit Quinquis, Kévin Da Silva, Florian Plaza Oñate, Nicolas Pons, Hugo Roume, Mircea Podar, and Mathieu Almeida. 2022. “Benchmarking Second and Third-Generation Sequencing Platforms for Microbial Metagenomics.” Scientific Data 9 (1): 694. doi: 10.1038/s41597-022-01762-z.
+  > Meslier, Victoria, Benoit Quinquis, Kévin Da Silva, Florian Plaza Oñate, Nicolas Pons, Hugo Roume, Mircea Podar, and Mathieu Almeida. 2022. “Benchmarking Second and Third-Generation Sequencing Platforms for Microbial Metagenomics.” Scientific Data 9 (1): 694. doi: 10.1038/s41597-022-01762-z.

bin/check_samplesheet.py

@@ -71,7 +71,6 @@ def check_samplesheet(file_in, file_out):
 
     sample_mapping_dict = {}
     with open(file_in, "r") as fin:
-
         ## Check header
         MIN_COLS = 4
         HEADER = [
@@ -101,7 +100,6 @@ def check_samplesheet(file_in, file_out):
 
         ## Check sample entries
         for line in fin:
-
             ## Pull out only relevant columns for downstream checking
             line_parsed = [x.strip().strip('"') for x in line.strip().split(",")]
 

conf/test_full.config

@@ -20,12 +20,12 @@ params {
     hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'
 
     save_preprocessed_reads = true
-     
+
     perform_shortread_qc = true
     shortread_qc_mergepairs = true
     perform_shortread_complexityfilter = true
     save_complexityfiltered_reads = true
-     
+
     perform_longread_qc = true
     perform_shortread_hostremoval = true
     perform_longread_hostremoval = true
@@ -46,20 +46,20 @@ params {
     run_kraken2 = true
     kraken2_save_reads = true
     kraken2_save_readclassification = true
-    kraken2_save_minimizers  = true 
-    
-    run_krakenuniq = true   
+    kraken2_save_minimizers  = true
+
+    run_krakenuniq = true
     krakenuniq_save_reads = true
     krakenuniq_save_readclassifications = true
 
     run_bracken = true
-    
+
     run_malt = true
     malt_save_reads = true
     malt_generate_megansummary = true
 
     run_metaphlan3 = true
-    
+
     run_motus = true
     motus_save_mgc_read_counts = true
 
@@ -67,4 +67,4 @@ params {
     run_krona = true
 }
 
-cleanup = true
+cleanup = true