Add larger test data and sample report

bin/read_lengths.py

@@ -1,18 +1,38 @@
 #!/usr/bin/env python
-
 import argparse
+import glob
+import itertools
+import os
 import pysam
+import numpy as np
+
+
+def mean_qual(quals):
+    qual = np.fromiter(
+        (ord(x) - 33 for x in quals),
+        dtype=int, count=len(quals))
+    mean_p = np.mean(np.power(10, qual / -10))
+    return -10 * np.log10(mean_p)
 
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('fasta')
-    parser.add_argument('output')
+    parser.add_argument("directory", help="Directory containing .fastq(.gz) files")
+    parser.add_argument("output", help="Output file")
     args = parser.parse_args()
 
-    with open(args.output, 'w') as fh:
-        for rec in pysam.FastxFile(args.fasta):
-            fh.write("{}\t{}\n".format(rec.name, len(rec.sequence)))
+    fastqs = glob.glob(os.path.join(args.directory, "*.fastq*"))
+    reads = itertools.chain.from_iterable(
+        pysam.FastxFile(fname) for fname in fastqs)
 
-if __name__ == '__main__':
+    with open(args.output, "w") as fh:
+        # names as in Guppy
+        fh.write("read_id\tsequence_length_template\tmean_qscore_template\n")
+        for read in reads:
+            fh.write("\t".join(str(x) for x in (
+                read.name, len(read.sequence), mean_qual(read.quality))))
+            fh.write("\n")
+
+
+if __name__ == "__main__":
     main()

bin/report.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+
+import argparse
+import glob
+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):
+    dfs = list()
+    for fname in sorted(summaries):
+        dfs.append(pd.read_csv(fname, sep="\t"))
+    return pd.concat(dfs)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("report", help="Report output file")
+    parser.add_argument("summaries", nargs='+', help="Read summary file.")
+    args = parser.parse_args()
+
+    report_doc = report.HTMLReport(
+        "Workflow Template Sequencing report",
+        "Results generated through the wf-template nextflow workflow by Oxford Nanopore Technologies")
+
+    report_doc.markdown('''
+### Read Quality control
+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)
+    total_bases = seq_summary['sequence_length_template'].sum()
+    mean_length = total_bases / len(seq_summary)
+    median_length = np.median(seq_summary['sequence_length_template'])
+    datas = [seq_summary['sequence_length_template']]
+    length_hist = hist.histogram(
+        datas, colors=[np_blue], bins=100,
+        title="Read length distribution.",
+        x_axis_label='Read Length / bases',
+        y_axis_label='Number of reads',
+        xlim=(0, 2000))
+    length_hist = annot.subtitle(
+        length_hist,
+        "Mean: {:.0f}. Median: {:.0f}".format(
+            mean_length, median_length))
+
+    datas = [seq_summary['mean_qscore_template']]
+    mean_q, median_q = np.mean(datas[0]), np.median(datas[0])
+    q_hist = hist.histogram(
+        datas, colors=[np_blue], bins=100,
+        title="Read quality score",
+        x_axis_label="Quality score",
+        y_axis_label="Number of reads",
+        xlim=(4, 25))
+    q_hist = annot.subtitle(
+        q_hist,
+        "Mean: {:.0f}. Median: {:.0f}".format(
+            mean_q, median_q))
+
+    report_doc.plot(gridplot([[length_hist, q_hist]]))
+
+    # Footer section
+    report_doc.markdown('''
+### About
+
+**Oxford Nanopore Technologies products are not intended for use for health 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).
+The workflow can be run using `nextflow epi2me-labs/wf-template --help`
+
+---
+''')
+
+    # write report
+    report_doc.write(args.report)
+
+if __name__ == "__main__":
+    main()

environment.yaml

@@ -4,5 +4,6 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    - python==3.6
+    - python==3.6.*
+    - aplanat
     - pysam

main.nf

@@ -18,10 +18,10 @@ def helpMessage(){
 Workflow template'
 
 Usage:
-    nextflow run epi2melabs/workflow-template [options]
+    nextflow run epi2melabs/wf-template [options]
 
 Script Options:
-    --fastq        FILE    Path to FASTQ file (required)
+    --fastq        DIR     Path to directory containing FASTQ files (required)
     --out_dir      DIR     Path for output (default: $params.out_dir)
 """
 }
@@ -37,11 +37,21 @@ process readSeqs {
 
     """
     read_lengths.py $reads seqs.txt
-    sleep 60
     """
 }
 
 
+process makeReport {
+    label "pysam"
+    input:
+        file "seqs.txt"
+    output:
+        file "report.html"
+    """
+    report.py report.html seqs.txt
+    """
+}
+
 
 // See https://github.com/nextflow-io/nextflow/issues/1636
 // This is the only way to publish files from a workflow whilst
@@ -65,9 +75,10 @@ workflow pipeline {
     take:
         reads
     main:
-        seqs = readSeqs(reads)
+        summary = readSeqs(reads)
+        report = makeReport(summary)
     emit:
-        seqs
+        summary.concat(report)
 }
 
 // entrypoint workflow
@@ -86,7 +97,12 @@ workflow {
     }
 
 
-    reads = channel.fromPath(params.fastq, checkIfExists:true)
-    results = pipeline(reads)
-    output(results)
+    reads = file("$params.fastq/*.fastq*", type: 'file', maxdepth: 1)
+    if (reads) {
+        reads = Channel.fromPath(params.fastq, type: 'dir', maxDepth: 1)
+        results = pipeline(reads)
+        output(results)
+    } else {
+        println("No .fastq(.gz) files found under `${params.fastq}`.")
+    }
 }

nextflow.config

@@ -36,7 +36,7 @@ profiles {
         }
         process {
             withLabel:pysam {
-                container = "ontresearch/workflow-template:${params.wfversion}"
+                container = "ontresearch/wf-template:${params.wfversion}"
             }
             shell = ['/bin/bash', '-euo', 'pipefail']
         }