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Alex Kanitz authored
- clean up command line interface - improve descriptions - add consistent structure - remove or merge superfluous CLI arguments - set defaults - update test calls - update docs - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table - allow user to specify environment variables and relative paths in input table and on CLI - relative paths in the input table are interpreted with respect to the directory containing the input table - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown - set STAR index size to read length - 1 - remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly - rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly - add logging - add docstrings to module and all functions - add typing definitions to all functions - restructure and comment code to improve readability - linters `flake8` and `mypy` pass
Alex Kanitz authored- clean up command line interface - improve descriptions - add consistent structure - remove or merge superfluous CLI arguments - set defaults - update test calls - update docs - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table - allow user to specify environment variables and relative paths in input table and on CLI - relative paths in the input table are interpreted with respect to the directory containing the input table - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown - set STAR index size to read length - 1 - remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly - rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly - add logging - add docstrings to module and all functions - add typing definitions to all functions - restructure and comment code to improve readability - linters `flake8` and `mypy` pass
samples_alfa.tsv 1.36 KiB
sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf genome sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya alfa_directionality alfa_plus alfa_minus
paired_end_R1_on_plus_sense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX GATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-firststrand str1 str2
paired_end_R1_on_plus_antisense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-secondstrand str2 str1
paired_end_R1_on_minus_sense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-firststrand str1 str2
paired_end_R1_on_minus_antisense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-secondstrand str2 str1