feat: add temp dir and code refactor

bio/mosdepth/test/Snakefile

@@ -4,14 +4,13 @@ rule mosdepth:
         bai="aligned/{dataset}.bam.bai",
     output:
         "mosdepth/{dataset}.mosdepth.global.dist.txt",
-        "mosdepth/{dataset}.per-base.bed.gz",  # produced unless --no-per-base specified
-        summary="mosdepth/{dataset}.mosdepth.summary.txt",  # this named output is required for prefix parsing
+        "mosdepth/{dataset}.per-base.bed.gz",
+        summary="mosdepth/{dataset}.mosdepth.summary.txt",
     log:
         "logs/mosdepth/{dataset}.log",
     params:
-        extra="--fast-mode",  # optional
-    # additional decompression threads through `--threads`
-    threads: 4  # This value - 1 will be sent to `--threads`
+        extra="--fast-mode",
+    threads: 4
     wrapper:
         "master/bio/mosdepth"
 
@@ -25,13 +24,12 @@ rule mosdepth_bed:
         "mosdepth_bed/{dataset}.mosdepth.global.dist.txt",
         "mosdepth_bed/{dataset}.mosdepth.region.dist.txt",
         "mosdepth_bed/{dataset}.regions.bed.gz",
-        summary="mosdepth_bed/{dataset}.mosdepth.summary.txt",  # this named output is required for prefix parsing
+        summary="mosdepth_bed/{dataset}.mosdepth.summary.txt",
     log:
         "logs/mosdepth_bed/{dataset}.log",
     params:
-        extra="--no-per-base --use-median",  # optional
-    # additional decompression threads through `--threads`
-    threads: 4  # This value - 1 will be sent to `--threads`
+        extra="--use-median",
+    threads: 4
     wrapper:
         "master/bio/mosdepth"
 
@@ -44,15 +42,14 @@ rule mosdepth_by_threshold:
         "mosdepth_by_threshold/{dataset}.mosdepth.global.dist.txt",
         "mosdepth_by_threshold/{dataset}.mosdepth.region.dist.txt",
         "mosdepth_by_threshold/{dataset}.regions.bed.gz",
-        "mosdepth_by_threshold/{dataset}.thresholds.bed.gz",  # needs to go with params.thresholds spec
-        summary="mosdepth_by_threshold/{dataset}.mosdepth.summary.txt",  # this named output is required for prefix parsing
+        "mosdepth_by_threshold/{dataset}.thresholds.bed.gz",
+        summary="mosdepth_by_threshold/{dataset}.mosdepth.summary.txt",
     log:
         "logs/mosdepth_by/{dataset}.log",
     params:
-        by="500",  # optional, window size,  specifies --by for mosdepth.region.dist.txt and regions.bed.gz
-        thresholds="1,5,10,30",  # optional, specifies --thresholds for thresholds.bed.gz
-    # additional decompression threads through `--threads`
-    threads: 4  # This value - 1 will be sent to `--threads`
+        by="500",  # needed for mosdepth.region.dist.txt and regions.bed.gz
+        thresholds="1,5,10,30",  # needed for thresholds.bed.gz
+    threads: 4
     wrapper:
         "master/bio/mosdepth"
 
@@ -63,16 +60,14 @@ rule mosdepth_quantize_precision:
         bai="aligned/{dataset}.bam.bai",
     output:
         "mosdepth_quantize_precision/{dataset}.mosdepth.global.dist.txt",
-        "mosdepth_quantize_precision/{dataset}.quantized.bed.gz",  # optional, needs to go with params.quantize spec
-        summary="mosdepth_quantize_precision/{dataset}.mosdepth.summary.txt",  # this named output is required for prefix parsing
+        "mosdepth_quantize_precision/{dataset}.quantized.bed.gz",
+        summary="mosdepth_quantize_precision/{dataset}.mosdepth.summary.txt",
     log:
         "logs/mosdepth_quantize_precision/{dataset}.log",
     params:
-        extra="--no-per-base",  # optional
-        quantize="0:1:5:150",  # optional, specifies --quantize for quantized.bed.gz
+        quantize="0:1:5:150",  # needed for quantized.bed.gz
         precision="5",  # optional, set decimals of precision
-    # additional decompression threads through `--threads`
-    threads: 4  # This value - 1 will be sent to `--threads`
+    threads: 4
     wrapper:
         "master/bio/mosdepth"
 
@@ -87,12 +82,11 @@ rule mosdepth_cram:
         "mosdepth_cram/{dataset}.mosdepth.global.dist.txt",
         "mosdepth_cram/{dataset}.mosdepth.region.dist.txt",
         "mosdepth_cram/{dataset}.regions.bed.gz",
-        summary="mosdepth_cram/{dataset}.mosdepth.summary.txt",  # this named output is required for prefix parsing
+        summary="mosdepth_cram/{dataset}.mosdepth.summary.txt",
     log:
         "logs/mosdepth_cram/{dataset}.log",
     params:
-        extra="--no-per-base --use-median",  # optional
-    # additional decompression threads through `--threads`
-    threads: 4  # This value - 1 will be sent to `--threads`
+        extra="--use-median",
+    threads: 4
     wrapper:
         "master/bio/mosdepth"

bio/mosdepth/test/test.bed

@@ -1 +1 @@
-ecoliK12_pbi_March2013	40645	40845
+Sheila	2	6

bio/mosdepth/wrapper.py

@@ -3,84 +3,50 @@
 __email__ = "wrowell@pacb.com"
 __license__ = "MIT"
 
-import sys
+
+import tempfile
 from snakemake.shell import shell
 
+
 extra = snakemake.params.get("extra", "")
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-
-bed = snakemake.input.get("bed", "")
-by = snakemake.params.get("by", "")
-if by:
-    if bed:
-        sys.exit(
-            "Either provide a bed input file OR a window size via params.by, not both."
-        )
-    else:
-        by = f"--by {by}"
-if bed:
-    by = f"--by {bed}"
-
-quantize_out = False
-thresholds_out = False
-regions_bed_out = False
-region_dist_out = False
+log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
+
+
+# Check output files
+per_base_out = quantize_out = thresholds_out = global_dist_out = region_dist_out = (
+    regions_bed_out
+) = False
 for file in snakemake.output:
-    if ".per-base." in file and "--no-per-base" in extra:
-        sys.exit(
-            "You asked not to generate per-base output (--no-per-base), but your rule specifies a '.per-base.' output file. Remove one of the two."
-        )
-    if ".quantized.bed.gz" in file:
-        quantize_out = True
-    if ".thresholds.bed.gz" in file:
-        thresholds_out = True
-    if ".mosdepth.region.dist.txt" in file:
-        region_dist_out = True
-    if ".regions.bed.gz" in file:
-        regions_bed_out = True
-
-
-if by and not regions_bed_out:
-    sys.exit(
-        "You ask for by-region output. Please also specify *.regions.bed.gz as a rule output."
-    )
+    if file.endswith(".per-base.bed.gz"):
+        per_base_out = file
+    if file.endswith(".quantized.bed.gz"):
+        quantize_out = file
+    if file.endswith(".thresholds.bed.gz"):
+        thresholds_out = file
+    if file.endswith(".mosdepth.global.dist.txt"):
+        global_dist_out = file
+    if file.endswith(".mosdepth.region.dist.txt"):
+        region_dist_out = file
+    if file.endswith(".regions.bed.gz"):
+        regions_bed_out = file
 
-if by and not region_dist_out:
-    sys.exit(
-        "You ask for by-region output. Please also specify *.mosdepth.region.dist.txt as a rule output."
-    )
 
-if (region_dist_out or regions_bed_out) and not by:
-    sys.exit(
-        "You specify *.regions.bed.gz and/or *.mosdepth.region.dist.txt as a rule output. You also need to ask for by-region output via 'input.bed' or 'params.by'."
-    )
+if not per_base_out:
+    extra += " --no-per-base"
 
-quantize = snakemake.params.get("quantize", "")
-if quantize:
-    if not quantize_out:
-        sys.exit(
-            "You ask for quantized output via params.quantize. Please also specify *.quantized.bed.gz as a rule output."
-        )
-    quantize = f"--quantize {quantize}"
 
-if not quantize and quantize_out:
-    sys.exit(
-        "The rule has output *.quantized.bed.gz specified. Please also specify params.quantize to actually generate it."
-    )
+if quantize_out:
+    extra += f" --quantize {snakemake.params.quantize}"
 
 
-thresholds = snakemake.params.get("thresholds", "")
-if thresholds:
-    if not thresholds_out:
-        sys.exit(
-            "You ask for --thresholds output via params.thresholds. Please also specify *.thresholds.bed.gz as a rule output."
-        )
-    thresholds = f"--thresholds {thresholds}"
+if thresholds_out:
+    extra += f" --thresholds {snakemake.params.thresholds}"
 
-if not thresholds and thresholds_out:
-    sys.exit(
-        "The rule has output *.thresholds.bed.gz specified. Please also specify params.thresholds to actually generate it."
-    )
+
+if region_dist_out or regions_bed_out:
+    by = snakemake.input.get("bed", snakemake.params.get("by", False))
+    if by:
+        extra += f" --by {by}"
 
 
 precision = snakemake.params.get("precision", "")
@@ -93,16 +59,38 @@
     fasta = f"--fasta {fasta}"
 
 
-# mosdepth takes additional threads through its option --threads
-# One thread for mosdepth
-# Other threads are *additional* decompression threads passed to the '--threads' argument
+# mosdepth uses additional threads for decompression, passed to the '--threads' argument
 threads = "" if snakemake.threads <= 1 else "--threads {}".format(snakemake.threads - 1)
 
 
-# named output summary = "*.mosdepth.summary.txt" is required
-prefix = snakemake.output.summary.replace(".mosdepth.summary.txt", "")
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "{precision} mosdepth {threads} {fasta} {extra} {tmpdir}/temp {snakemake.input.bam} {log}"
+    )
+
+    if snakemake.output.get("summary"):
+        shell(
+            "mv --verbose {tmpdir}/temp.mosdepth.summary.txt {snakemake.output.summary} {log}"
+        )
+
+    if per_base_out:
+        shell("mv --verbose {tmpdir}/temp.per-base.bed.gz {per_base_out} {log}")
 
+    if quantize_out:
+        shell("mv --verbose {tmpdir}/temp.quantized.bed.gz {quantize_out} {log}")
+
+    if thresholds_out:
+        shell("mv --verbose {tmpdir}/temp.thresholds.bed.gz {thresholds_out} {log}")
+
+    if global_dist_out:
+        shell(
+            "mv --verbose {tmpdir}/temp.mosdepth.global.dist.txt {global_dist_out} {log}"
+        )
+
+    if region_dist_out:
+        shell(
+            "mv --verbose {tmpdir}/temp.mosdepth.region.dist.txt {region_dist_out} {log}"
+        )
 
-shell(
-    "({precision} mosdepth {threads} {fasta} {by} {quantize} {thresholds} {extra} {prefix} {snakemake.input.bam}) {log}"
-)
+    if regions_bed_out:
+        shell("mv --verbose {tmpdir}/temp.regions.bed.gz {regions_bed_out} {log}")

test_wrappers.py

@@ -3752,61 +3752,9 @@ def test_mosdepth(run):
             "--cores",
             "4",
             "mosdepth/m54075_180905_225130.ccs.ecoliK12_pbi_March2013.mosdepth.summary.txt",
-            "--use-conda",
-            "-F",
-        ],
-    )
-
-
-def test_mosdepth_bed(run):
-    run(
-        "bio/mosdepth",
-        [
-            "snakemake",
-            "--cores",
-            "4",
             "mosdepth_bed/m54075_180905_225130.ccs.ecoliK12_pbi_March2013.mosdepth.summary.txt",
-            "--use-conda",
-            "-F",
-        ],
-    )
-
-
-def test_mosdepth_by_threshold(run):
-    run(
-        "bio/mosdepth",
-        [
-            "snakemake",
-            "--cores",
-            "4",
             "mosdepth_by_threshold/m54075_180905_225130.ccs.ecoliK12_pbi_March2013.mosdepth.summary.txt",
-            "--use-conda",
-            "-F",
-        ],
-    )
-
-
-def test_mosdepth_quantize_precision(run):
-    run(
-        "bio/mosdepth",
-        [
-            "snakemake",
-            "--cores",
-            "4",
             "mosdepth_quantize_precision/m54075_180905_225130.ccs.ecoliK12_pbi_March2013.mosdepth.summary.txt",
-            "--use-conda",
-            "-F",
-        ],
-    )
-
-
-def test_mosdepth_cram(run):
-    run(
-        "bio/mosdepth",
-        [
-            "snakemake",
-            "--cores",
-            "4",
             "mosdepth_cram/a.mosdepth.summary.txt",
             "--use-conda",
             "-F",