Merge branch 'newtemp' into 'dev'

Newtemp

See merge request epi2melabs/workflow-containers/wf-template!10

.gitlab-ci.yml

@@ -1,18 +1,12 @@
+# Include shared CI
 include:
     - project: "epi2melabs/ci-templates"
       file: "wf-containers.yaml"
 
-.run: &run |
+variables:
-    ${NEXTFLOWRUN} -w ${OUTPUT}/workspace --out_dir ${OUTPUT} \
+    # Workflow inputs given to nextflow.
-        --fastq test_data
+    # The workflow should define `--out_dir`, the CI template sets this.
+    # Only common file inputs and option values need to be given here
+    # (not things such as -profile)
+    NF_WORKFLOW_OPTS: "--fastq test_data"
 
-conda-run:
-    extends: .conda-run
-    script:
-        - *run
-
-docker-run:
-    extends: .docker-run
-    script:
-        - *run
-        - touch ${CI_PROJECT_DIR}/success

bin/read_lengths.py

@@ -1,13 +1,17 @@
 #!/usr/bin/env python
+"""Create a simple summary of a fastq file."""
+
 import argparse
 import glob
 import itertools
 import os
-import pysam
+
 import numpy as np
+import pysam
 
 
 def mean_qual(quals):
+    """Calculate mean quality of a read."""
     qual = np.fromiter(
         (ord(x) - 33 for x in quals),
         dtype=int, count=len(quals))
@@ -16,9 +20,12 @@ def mean_qual(quals):
 
 
 def main():
+    """Run entry point."""
     parser = argparse.ArgumentParser()
-    parser.add_argument("directory", help="Directory containing .fastq(.gz) files")
+    parser.add_argument(
-    parser.add_argument("output", help="Output file")
+        "directory", help="Directory containing .fastq(.gz) files")
+    parser.add_argument(
+        "output", help="Output file")
     args = parser.parse_args()
 
     fastqs = glob.glob(os.path.join(args.directory, "*.fastq*"))

bin/report.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python
+"""Create workflow report."""
 
 import argparse
-import glob
+
+from aplanat import annot, hist, report
+from bokeh.layouts import gridplot
 import numpy as np
 import pandas as pd
 
-from bokeh.layouts import gridplot, layout
-import aplanat
-from aplanat import annot, hist, report
-
 
 def read_files(summaries):
+    """Combine a list of files into a single dataframe."""
     dfs = list()
     for fname in sorted(summaries):
         dfs.append(pd.read_csv(fname, sep="\t"))
@@ -18,6 +18,7 @@ def read_files(summaries):
 
 
 def main():
+    """Run the entry point."""
     parser = argparse.ArgumentParser()
     parser.add_argument("report", help="Report output file")
     parser.add_argument("summaries", nargs='+', help="Read summary file.")
@@ -25,7 +26,8 @@ def main():
 
     report_doc = report.HTMLReport(
         "Workflow Template Sequencing report",
-        "Results generated through the wf-template nextflow workflow by Oxford Nanopore Technologies")
+        ("Results generated through the wf-template nextflow "
+            "workflow by Oxford Nanopore Technologies"))
 
     report_doc.markdown('''
 ### Read Quality control
@@ -33,8 +35,6 @@ This section displays basic QC metrics indicating read data quality.
 ''')
 
     np_blue = '#0084A9'
-    np_dark_grey = '#455560'
-    np_light_blue = '#90C6E7'
 
     # read length summary
     seq_summary = read_files(args.summaries)
@@ -72,11 +72,13 @@ This section displays basic QC metrics indicating read data quality.
     report_doc.markdown('''
 ### About
 
-**Oxford Nanopore Technologies products are not intended for use for health assessment
+**Oxford Nanopore Technologies products are not intended for use for health
-or to diagnose, treat, mitigate, cure or prevent any disease or condition.**
+assessment or to diagnose, treat, mitigate, cure or prevent any disease or
+condition.**
 
-This report was produced using the [epi2me-labs/wf-template](https://github.com/epi2me-labs/wf-template).
+This report was produced using the
-The workflow can be run using `nextflow epi2me-labs/wf-template --help`
+[epi2me-labs/wf-template](https://github.com/epi2me-labs/wf-template).  The
+workflow can be run using `nextflow epi2me-labs/wf-template --help`
 
 ---
 ''')
@@ -84,5 +86,6 @@ The workflow can be run using `nextflow epi2me-labs/wf-template --help`
     # write report
     report_doc.write(args.report)
 
+
 if __name__ == "__main__":
     main()