Dev

pixi.toml

@@ -38,7 +38,6 @@ test = { cmd = [
 ], depends-on = [
     "test-data",
 ], clean-env = true }
-
 fire = { cmd = [
     "cd",
     "$INIT_CWD",

workflow/Snakefile

@@ -19,7 +19,14 @@ include: "rules/common.smk"
 
 
 # load the version from the environment
-VERSION = f"v{os.environ.get("PIXI_PROJECT_VERSION", "UNK")}"
+FULL_VERSION = f"v{os.environ.get("PIXI_PROJECT_VERSION", "UNK")}"
+# trim the FULL_VERSION to just the just the major and minor version
+VERSION = ".".join(FULL_VERSION.split(".")[:2])
+
+# use the full version if requested 
+if config.get("full-version", False):
+    VERSION = FULL_VERSION
+
 
 # thread options
 MAX_THREADS = config.get("max_threads", 4)

workflow/envs/env.yaml

@@ -13,4 +13,4 @@ dependencies:
   - ripgrep
   - csvtk
   - mosdepth==0.3.7
-  - bioconda::bigtools==0.5.4
+  - bioconda::bigtools==0.5.5

workflow/rules/decorated-reads.smk

@@ -14,6 +14,8 @@ rule decorate_fibers_chromosome:
     threads: 4
     resources:
         mem_mb=get_mem_mb,
+    # the following steps can take a while so this helps the pipeline start this earlier.
+    priority: 10
     conda:
         DEFAULT_ENV
     shell:
@@ -42,6 +44,7 @@ rule decorate_fibers_1:
     threads: 8
     resources:
         runtime=240,
+    priority: 10
     conda:
         DEFAULT_ENV
     params:
@@ -55,7 +58,7 @@ rule decorate_fibers_1:
         cat {input.bed} \
             | bgzip -cd -@ {threads} \
             | bigtools bedtobigbed \
-                --inmemory \
+                --inmemory -t {threads} \
                 --block-size {params.block_size} --items-per-slot {params.items_per_slot} \
                 --nzooms {params.nzooms} \
                 -s start -a {params.bed_as} \
@@ -79,6 +82,7 @@ rule decorate_fibers_2:
     threads: 8
     resources:
         runtime=60 * 16,
+    priority: 10
     conda:
         DEFAULT_ENV
     params:
@@ -96,10 +100,10 @@ rule decorate_fibers_2:
             | rg -v '^#' \
             | rg -vw 'NUC' \
             | bigtools bedtobigbed \
-                --inmemory \
+                --inmemory -t {threads} \
                 --block-size {params.block_size} --items-per-slot {params.items_per_slot} \
                 --nzooms {params.nzooms} \
-                -a {params.dec_as} -s start \
+                -s start -a {params.dec_as} \
                 - {input.fai} {output.bb}
         """
 

workflow/rules/fire-peaks.smk

@@ -77,7 +77,7 @@ rule fdr_table:
     params:
         script=workflow.source_path("../scripts/fdr-table.py"),
     resources:
-        mem_mb=get_mem_mb,
+        mem_mb=get_mem_mb_xl,
     shell:
         """
         MIN=$(cat {input.minimum})