Merge pull request #116 from nf-core/nf-core-template-merge-2.5.1

Important! Template update for nf-core/tools v2.5.1

.github/workflows/ci.yml

@@ -55,11 +55,10 @@ jobs:
           sudo update-locale LANG=en_US.UTF-8
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
+        uses: Wandalen/wretry.action@v1.0.11
-        # For example: adding multiple test runs with different parameters
+        with:
-        # Remember that you can parallelise this by using strategy.matrix
+          command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
-        run: |
+          attempt_limit: 3
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
 
   motus:
     name: Test mOTUs with workflow parameters
@@ -79,14 +78,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install Nextflow
-        env:
+        uses: nf-core/setup-nextflow@v1
-          NXF_VER: ${{ matrix.NXF_VER }}
+        with:
-          # Uncomment only if the edge release is more recent than the latest stable release
+          version: "${{ matrix.NXF_VER }}"
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
 
       - name: Show current locale
         run: locale

bin/check_samplesheet.py

@@ -6,10 +6,10 @@ import sys
 import errno
 import argparse
 
+
 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>"
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
@@ -17,6 +17,7 @@ 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:
@@ -25,6 +26,7 @@ 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 != "":
@@ -34,6 +36,7 @@ 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:
@@ -117,9 +120,7 @@ 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(
+                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
-                        MIN_COLS
-                    ),
                     "Line",
                     line,
                 )
@@ -182,13 +183,9 @@ 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 (
+            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])
-            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])
             elif fasta and (fastq_1 or fastq_2):
                 print_error(

pyproject.toml

@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3