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Revert "Fix final linting problems for template merge"

This reverts commit e64b3f85a4.
This commit is contained in:
James Fellows Yates 2022-09-02 11:47:33 +02:00
parent 61560cf065
commit 8fe7f8bf4b
2 changed files with 110 additions and 142 deletions

View file

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

View file

@ -3,140 +3,104 @@
"homePage": "https://github.com/nf-core/taxprofiler",
"repos": {
"nf-core/modules": {
"git_url": "https://github.com/nf-core/modules.git",
"modules": {
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"branch": "master",
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},
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"branch": "master",
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"bowtie2/align": {
"branch": "master",
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"bowtie2/build": {
"branch": "master",
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"cat/fastq": {
"branch": "master",
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"centrifuge/centrifuge": {
"branch": "master",
"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
},
"centrifuge/kreport": {
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"git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
},
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},
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"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
},
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},
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},
"filtlong": {
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},
"gunzip": {
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
"motus/profile": {
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},
"multiqc": {
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},
"prinseqplusplus": {
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},
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},
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},
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}
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}
}