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Code Issues Releases Packages Activity

Black linting I hope

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This commit is contained in:
James Fellows Yates 2022-09-02 11:55:19 +02:00
parent 7917e1d656
commit 3a33d81e80
1 changed files with 8 additions and 12 deletions
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20
bin/check_samplesheet.py
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@ -6,10 +6,9 @@ import sys
import errno import errno
import argparse import argparse
def parse_args(args=None): def parse_args(args=None):
Description = ( Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
"Reformat nf-core/taxprofiler samplesheet file and check its contents."
)
Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>" Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
@ -18,6 +17,7 @@ def parse_args(args=None):
parser.add_argument("FILE_OUT", help="Output file.") parser.add_argument("FILE_OUT", help="Output file.")
return parser.parse_args(args) return parser.parse_args(args)
def make_dir(path): def make_dir(path):
if len(path) > 0: if len(path) > 0:
try: try:
@ -26,6 +26,7 @@ def make_dir(path):
if exception.errno != errno.EEXIST: if exception.errno != errno.EEXIST:
raise exception raise exception
def print_error(error, context="Line", context_str=""): def print_error(error, context="Line", context_str=""):
error_str = "ERROR: Please check samplesheet -> {}".format(error) error_str = "ERROR: Please check samplesheet -> {}".format(error)
if context != "" and context_str != "": if context != "" and context_str != "":
@ -35,6 +36,7 @@ def print_error(error, context="Line", context_str=""):
print(error_str) print(error_str)
sys.exit(1) sys.exit(1)
def check_samplesheet(file_in, file_out): def check_samplesheet(file_in, file_out):
""" """
This function checks that the samplesheet follows the following structure: This function checks that the samplesheet follows the following structure:
@ -118,9 +120,7 @@ def check_samplesheet(file_in, file_out):
num_cols = len([x for x in lspl if x]) num_cols = len([x for x in lspl if x])
if num_cols < MIN_COLS: if num_cols < MIN_COLS:
print_error( print_error(
"Invalid number of populated columns (minimum = {})!".format( "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
MIN_COLS
),
"Line", "Line",
line, line,
) )
@ -183,13 +183,9 @@ def check_samplesheet(file_in, file_out):
## Auto-detect paired-end/single-end ## Auto-detect paired-end/single-end
if sample and fastq_1 and fastq_2: ## Paired-end short reads if sample and fastq_1 and fastq_2: ## Paired-end short reads
sample_info.extend(["0", fastq_1, fastq_2, fasta]) sample_info.extend(["0", fastq_1, fastq_2, fasta])
elif ( elif sample and fastq_1 and not fastq_2: ## Single-end short/long fastq reads
sample and fastq_1 and not fastq_2
): ## Single-end short/long fastq reads
sample_info.extend(["1", fastq_1, fastq_2, fasta]) sample_info.extend(["1", fastq_1, fastq_2, fasta])
elif ( elif sample and fasta and not fastq_1 and not fastq_2: ## Single-end long reads
sample and fasta and not fastq_1 and not fastq_2
): ## Single-end long reads
sample_info.extend(["1", fastq_1, fastq_2, fasta]) sample_info.extend(["1", fastq_1, fastq_2, fasta])
elif fasta and (fastq_1 or fastq_2): elif fasta and (fastq_1 or fastq_2):
print_error( print_error(