diff --git a/pixi.toml b/pixi.toml index 080eedf31..431ab05e7 100644 --- a/pixi.toml +++ b/pixi.toml @@ -38,7 +38,6 @@ test = { cmd = [ ], depends-on = [ "test-data", ], clean-env = true } - fire = { cmd = [ "cd", "$INIT_CWD", diff --git a/workflow/Snakefile b/workflow/Snakefile index 3322c700a..f36e0da1c 100644 --- a/workflow/Snakefile +++ b/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) diff --git a/workflow/envs/env.yaml b/workflow/envs/env.yaml index 04b2f46b2..07984df4c 100644 --- a/workflow/envs/env.yaml +++ b/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 diff --git a/workflow/rules/decorated-reads.smk b/workflow/rules/decorated-reads.smk index 344218596..b39eb5f6f 100644 --- a/workflow/rules/decorated-reads.smk +++ b/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} """ diff --git a/workflow/rules/fire-peaks.smk b/workflow/rules/fire-peaks.smk index 6d5f2428d..07d15e0f6 100644 --- a/workflow/rules/fire-peaks.smk +++ b/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})