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Auto-generated via {sandpaper} Source : 0c69edc Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2024-04-25 14:15:22 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : cbe6adb Branch : main Author : Graeme Grimes <[email protected]> Time : 2024-04-25 14:13:53 +0000 Message : Merge pull request #145 from carpentries-incubator/pythoncode Pythoncode
carpentries-incubator · Apr 25, 2024 · 1241c38 · 1241c38
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commit 1241c38
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diff --git a/04-processes-part1.html b/04-processes-part1.html
diff --git a/06-workflow.html b/06-workflow.html
diff --git a/08-reporting.html b/08-reporting.html
diff --git a/aio.html b/aio.html
diff --git a/files/scripts/process/process_python_script.nf b/files/scripts/process/process_python_script.nf
@@ -0,0 +1,14 @@
+//process_python_script.nf
+nextflow.enable.dsl=2
+
+process PROCESS_READS {
+
+  script:
+  """
+  process_reads.py ${projectDir}/data/yeast/reads/ref1_1.fq.gz
+  """
+}
+
+workflow {
+  PROCESS_READS()
+}
diff --git a/files/scripts/process/process_reads.py b/files/scripts/process/process_reads.py
@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+import gzip
+import sys
+reads = 0
+bases = 0
+
+# Read gzipped fastq file
+with gzip.open(sys.argv[1], 'rb') as read:
+    for id in read:
+      seq = next(read)
+      reads += 1
+      bases += len(seq.strip())
+      next(read)
+      next(read)
+
+print("reads", reads)
+print("bases", bases)