init: split link_input_files into LR/SR (better for updates, no effect on output)

workflow/rules/init.smk

@@ -41,27 +41,33 @@ READ_ASSEMBLER_PAIRS = assembler_pairs(READ_ASSEMBLERS)
 BWA_IDX_EXT = ["amb", "ann", "bwt", "pac", "sa"]
 
 # Set links to input files
-localrules: link_input_files
+localrules: link_input_files_lr, link_input_files_sr
 
-rule link_input_files:
+rule link_input_files_lr:
     output:
-        metag_lr=os.path.join(RESULTS_DIR, "preproc/metag/lr/lr.fastq.gz"),
-        metag_sr=expand(os.path.join(RESULTS_DIR, "input/metag/sr/{rid}.fq.gz"), rid={"R1", "R2"}),
-        metat_sr=expand(os.path.join(RESULTS_DIR, "input/metat/sr/{rid}.fq.gz"), rid={"R1", "R2"}) if "metat" in META_TYPES else []
+        metag_lr=os.path.join(RESULTS_DIR, "preproc/metag/lr/lr.fastq.gz")
     message:
-        "Link input files"
+        "Link input files: LR"
     run:
         import os
         from pathlib import Path
-        # metaG, FASTQ
         ifname = os.path.abspath(config["data"]["metag"]["ont"]["fastq"])
         ofname = os.path.join(RESULTS_DIR, "preproc/metag/lr/lr.fastq.gz")
         os.symlink(os.path.abspath(ifname), ofname, target_is_directory=False)
+
+rule link_input_files_sr:
+    output:
+        metag_sr=expand(os.path.join(RESULTS_DIR, "input/metag/sr/{rid}.fq.gz"), rid={"R1", "R2"}),
+        metat_sr=expand(os.path.join(RESULTS_DIR, "input/metat/sr/{rid}.fq.gz"), rid={"R1", "R2"}) if "metat" in META_TYPES else []
+    message:
+        "Link input files: SR"
+    run:
+        import os
+        from pathlib import Path
         # metaG, SR
         os.symlink(os.path.abspath(config["data"]["metag"]["sr"]["r1"]), os.path.join(RESULTS_DIR, "input/metag/sr/R1.fq.gz"), target_is_directory=False)
         os.symlink(os.path.abspath(config["data"]["metag"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metag/sr/R2.fq.gz"), target_is_directory=False)
         # metaT, SR
         if "metat" in META_TYPES:
             os.symlink(os.path.abspath(config["data"]["metat"]["sr"]["r1"]), os.path.join(RESULTS_DIR, "input/metat/sr/R1.fq.gz"), target_is_directory=False)
-            os.symlink(os.path.abspath(config["data"]["metat"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metat/sr/R2.fq.gz"), target_is_directory=False)
-    
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+            os.symlink(os.path.abspath(config["data"]["metat"]["sr"]["r2"]), os.path.join(RESULTS_DIR, "input/metat/sr/R2.fq.gz"), target_is_directory=False)
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