Snakefile to prepare data submission.

It creates links in a directory hierarchy from a configuration file.

Data_submission/Data_submission.snakefile

+import sys
+
+
+major, minor = sys.version_info[:2]
+if major < 3 or (major == 3 and minor < 6):
+    sys.exit("Need at least python 3.6\n")
+
+
+import os
+
+
+OPJ = os.path.join
+
+
+from pathlib import Path
+
+
+ref_info = config["ref"]
+data_dir = ref_info["paper"]
+
+data_info = config["data"]
+
+
+def determine_fqgz_and_md5file():
+    for (lib_type, analyses) in data_info.items():
+        for (analysis, analysis_info) in analyses.items():
+            for (library, raw_data) in analysis_info["libraries"].items():
+                assert Path(raw_data).exists()
+                yield (
+                    OPJ(data_dir, lib_type, analysis, f"{library}.fastq.gz"),
+                    OPJ(data_dir, lib_type, analysis, f"{library}.fastq.gz.md5"))
+
+
+def lib2data(wildcards):
+    return data_info[wildcards.lib_type][wildcards.analysis]["libraries"][wildcards.library]
+
+
+rule all:
+    input:
+        list(zip(*determine_fqgz_and_md5file()))
+
+
+rule link_raw_data:
+    """This rule installs the raw data in a local directory using symlinks.
+    The location of the original files is taken from the configuration."""
+    input:
+        raw = lib2data,
+    output:
+        link = os.path.join(data_dir, "{lib_type}/{analysis}/{library}.fastq.gz")
+    message:
+        "Making link {output.link} to raw data {input.raw}."
+    run:
+        os.symlink(os.path.abspath(input.raw), output.link)
+
+
+rule compute_md5sum:
+    """This rule installs the raw data in a local directory using symlinks.
+    The location of the original files is taken from the configuration."""
+    input:
+        link = rules.link_raw_data.output.link,
+    output:
+        md5 = os.path.join(data_dir, "{lib_type}/{analysis}/{library}.fastq.gz.md5")
+    message:
+        "Computing md5sum for {input.link}."
+    shell:
+        """
+        md5sum {input.link} > {output.md5}
+        """