mirror of
https://github.com/MillironX/taxprofiler.git
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Merge pull request #116 from nf-core/nf-core-template-merge-2.5.1
Important! Template update for nf-core/tools v2.5.1
This commit is contained in:
commit
c9a7797682
3 changed files with 26 additions and 25 deletions
20
.github/workflows/ci.yml
vendored
20
.github/workflows/ci.yml
vendored
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@ -55,11 +55,10 @@ jobs:
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sudo update-locale LANG=en_US.UTF-8
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sudo update-locale LANG=en_US.UTF-8
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- name: Run pipeline with test data
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- name: Run pipeline with test data
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# TODO nf-core: You can customise CI pipeline run tests as required
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uses: Wandalen/wretry.action@v1.0.11
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# For example: adding multiple test runs with different parameters
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with:
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# Remember that you can parallelise this by using strategy.matrix
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command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
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run: |
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attempt_limit: 3
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
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motus:
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motus:
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name: Test mOTUs with workflow parameters
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name: Test mOTUs with workflow parameters
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@ -79,14 +78,9 @@ jobs:
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uses: actions/checkout@v2
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uses: actions/checkout@v2
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- name: Install Nextflow
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- name: Install Nextflow
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env:
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uses: nf-core/setup-nextflow@v1
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NXF_VER: ${{ matrix.NXF_VER }}
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with:
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# Uncomment only if the edge release is more recent than the latest stable release
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version: "${{ matrix.NXF_VER }}"
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Show current locale
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- name: Show current locale
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run: locale
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run: locale
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@ -6,10 +6,10 @@ import sys
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import errno
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import errno
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import argparse
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import argparse
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def parse_args(args=None):
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def parse_args(args=None):
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Description = (
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Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
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"Reformat nf-core/taxprofiler samplesheet file and check its contents."
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)
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Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
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Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
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parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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@ -17,6 +17,7 @@ def parse_args(args=None):
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parser.add_argument("FILE_OUT", help="Output file.")
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parser.add_argument("FILE_OUT", help="Output file.")
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return parser.parse_args(args)
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return parser.parse_args(args)
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def make_dir(path):
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def make_dir(path):
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if len(path) > 0:
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if len(path) > 0:
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try:
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try:
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@ -25,6 +26,7 @@ def make_dir(path):
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if exception.errno != errno.EEXIST:
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if exception.errno != errno.EEXIST:
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raise exception
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raise exception
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def print_error(error, context="Line", context_str=""):
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def print_error(error, context="Line", context_str=""):
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error_str = "ERROR: Please check samplesheet -> {}".format(error)
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error_str = "ERROR: Please check samplesheet -> {}".format(error)
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if context != "" and context_str != "":
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if context != "" and context_str != "":
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@ -34,6 +36,7 @@ def print_error(error, context="Line", context_str=""):
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print(error_str)
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print(error_str)
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sys.exit(1)
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sys.exit(1)
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def check_samplesheet(file_in, file_out):
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def check_samplesheet(file_in, file_out):
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"""
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"""
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This function checks that the samplesheet follows the following structure:
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This function checks that the samplesheet follows the following structure:
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@ -117,9 +120,7 @@ def check_samplesheet(file_in, file_out):
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num_cols = len([x for x in lspl if x])
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num_cols = len([x for x in lspl if x])
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if num_cols < MIN_COLS:
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if num_cols < MIN_COLS:
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print_error(
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print_error(
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"Invalid number of populated columns (minimum = {})!".format(
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"Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
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MIN_COLS
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),
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"Line",
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"Line",
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line,
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line,
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)
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)
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@ -182,13 +183,9 @@ def check_samplesheet(file_in, file_out):
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## Auto-detect paired-end/single-end
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## Auto-detect paired-end/single-end
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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elif (
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elif sample and fastq_1 and not fastq_2: ## Single-end short/long fastq reads
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sample and fastq_1 and not fastq_2
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): ## Single-end short/long fastq reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif (
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elif sample and fasta and not fastq_1 and not fastq_2: ## Single-end long reads
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sample and fasta and not fastq_1 and not fastq_2
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): ## Single-end long reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif fasta and (fastq_1 or fastq_2):
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elif fasta and (fastq_1 or fastq_2):
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print_error(
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print_error(
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10
pyproject.toml
Normal file
10
pyproject.toml
Normal file
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@ -0,0 +1,10 @@
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# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
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# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
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[tool.black]
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line-length = 120
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target_version = ["py37", "py38", "py39", "py310"]
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[tool.isort]
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profile = "black"
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known_first_party = ["nf_core"]
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multi_line_output = 3
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