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Code Issues Releases Packages Activity

Fix linting

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James Fellows Yates 2023-02-02 13:08:16 +01:00
parent c4e366d47d
commit 7ce55a99e8
3 changed files with 9 additions and 11 deletions
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2
CITATIONS.md
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@ -101,4 +101,4 @@
- [Meslier (2022)](https://doi.org/10.1038/s41597-022-01762-z) (AWS Full Test data) - [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.

2
bin/check_samplesheet.py
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@ -71,7 +71,6 @@ def check_samplesheet(file_in, file_out):
sample_mapping_dict = {} sample_mapping_dict = {}
with open(file_in, "r") as fin: with open(file_in, "r") as fin:
## Check header ## Check header
MIN_COLS = 4 MIN_COLS = 4
HEADER = [ HEADER = [
@ -101,7 +100,6 @@ def check_samplesheet(file_in, file_out):
## Check sample entries ## Check sample entries
for line in fin: for line in fin:
## Pull out only relevant columns for downstream checking ## Pull out only relevant columns for downstream checking
line_parsed = [x.strip().strip('"') for x in line.strip().split(",")] line_parsed = [x.strip().strip('"') for x in line.strip().split(",")]

16
conf/test_full.config
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@ -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' 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 save_preprocessed_reads = true
perform_shortread_qc = true perform_shortread_qc = true
shortread_qc_mergepairs = true shortread_qc_mergepairs = true
perform_shortread_complexityfilter = true perform_shortread_complexityfilter = true
save_complexityfiltered_reads = true save_complexityfiltered_reads = true
perform_longread_qc = true perform_longread_qc = true
perform_shortread_hostremoval = true perform_shortread_hostremoval = true
perform_longread_hostremoval = true perform_longread_hostremoval = true
@ -46,20 +46,20 @@ params {
run_kraken2 = true run_kraken2 = true
kraken2_save_reads = true kraken2_save_reads = true
kraken2_save_readclassification = true kraken2_save_readclassification = true
kraken2_save_minimizers = true kraken2_save_minimizers = true
run_krakenuniq = true run_krakenuniq = true
krakenuniq_save_reads = true krakenuniq_save_reads = true
krakenuniq_save_readclassifications = true krakenuniq_save_readclassifications = true
run_bracken = true run_bracken = true
run_malt = true run_malt = true
malt_save_reads = true malt_save_reads = true
malt_generate_megansummary = true malt_generate_megansummary = true
run_metaphlan3 = true run_metaphlan3 = true
run_motus = true run_motus = true
motus_save_mgc_read_counts = true motus_save_mgc_read_counts = true
@ -67,4 +67,4 @@ params {
run_krona = true run_krona = true
} }
cleanup = true cleanup = true