diff --git a/CITATIONS.md b/CITATIONS.md index 825a2f9..2f75fdb 100644 --- a/CITATIONS.md +++ b/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. \ No newline at end of file + > 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. diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index f5b0e6a..9f0f7a6 100755 --- a/bin/check_samplesheet.py +++ b/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(",")] diff --git a/conf/test_full.config b/conf/test_full.config index cf8d873..07099d0 100644 --- a/conf/test_full.config +++ b/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 \ No newline at end of file +cleanup = true