biopipen 0.29.2__py3-none-any.whl → 0.31.0__py3-none-any.whl

biopipen/scripts/vcf/TruvariConsistency.R

@@ -1,4 +1,4 @@
-source("{{biopipen_dir}}/utils/plot.R")
+{{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 # to compile the expressions
 library(ComplexHeatmap)
 

biopipen/scripts/web/GCloudStorageDownloadBucket.py

@@ -0,0 +1,82 @@
+import concurrent.futures
+from pathlib import Path
+
+from biopipen.utils.misc import run_command, dict_to_cli_args, logger
+from biopipen.scripts.web.gcloud_common import (
+    is_logged_in,
+    is_valid_gs_bucket_url,
+    get_file_path,
+)
+
+url = {{in.url | repr}}  # pyright: ignore  # noqa: E999
+outdir = Path({{out.outdir | repr}})  # pyright: ignore
+gcloud = {{envs.gcloud | repr}}  # pyright: ignore
+keep_structure = {{envs.keep_structure | repr}}  # pyright: ignore
+ncores = {{envs.ncores | repr}}  # pyright: ignore
+args = {{envs.args | repr}}  # pyright: ignore
+
+if not is_valid_gs_bucket_url(url):
+    raise Exception(
+        f"Invalid Google Cloud Storage URL for a bucket: {url}. "
+        "URL should be in the format gs://bucket"
+    )
+
+if not is_logged_in(gcloud):
+    raise Exception(
+        "You need to be logged in to gcloud to download files. "
+        "Please run `gcloud auth login` first."
+    )
+
+
+def create_folders(folder_lines):
+    for folder_line in folder_lines:
+        folder_path = get_file_path(folder_line)
+        folder = outdir / folder_path
+        folder.mkdir(parents=True, exist_ok=True)
+
+
+def download_file(i: int, line: str, total: int):
+    path = get_file_path(line)
+
+    if total <= 50:
+        logger.info(f"Downloading {path}")
+    elif 50 < total <= 500:
+        if i % 10 == 0:
+            logger.info(f"Downloading {i}/{total} ...")
+    else:
+        if i % 100 == 0:
+            logger.info(f"Downloading {i}/{total} ...")
+
+    if keep_structure:
+        target = (outdir / path)
+    else:
+        name = Path(path).name
+        target = outdir / name
+        if target.exists():
+            new_name = f"g{i}-{name}"
+            logger.warning(f"{name} already exists. Renaming to {new_name}.")
+            target = outdir / new_name
+
+    gs_args = args.copy()
+    gs_args[""] = [gcloud, "storage", "cp", line, target]
+    run_command(dict_to_cli_args(gs_args, dashify=True), fg=True)
+
+
+def download_bucket():
+    out = run_command([gcloud, "storage", "ls", "--recursive", url], stdout="RETURN")
+    # remove empty lines and skip the root
+    out = list(filter(None, out.splitlines()[1:]))
+    if keep_structure:
+        # create folders first
+        logger.info(f"Creating folders to keep structure.")
+        folder_lines = [line[:-2] for line in out if line.endswith("/:")]
+        create_folders(folder_lines)
+
+    out = [line for line in out if not line.endswith("/:")]
+    length = len(out)
+    with concurrent.futures.ProcessPoolExecutor(max_workers=ncores) as executor:
+        executor.map(download_file, range(length), out, [length] * length)
+
+
+if __name__ == "__main__":
+    download_bucket()

biopipen/scripts/web/GCloudStorageDownloadFile.py

@@ -0,0 +1,23 @@
+from biopipen.utils.misc import run_command, dict_to_cli_args
+from biopipen.scripts.web.gcloud_common import is_logged_in, is_valid_gs_file_url
+
+url = {{in.url | repr}}  # pyright: ignore  # noqa: E999
+outfile = {{out.outfile | repr}}  # pyright: ignore
+gcloud = {{envs.gcloud | repr}}  # pyright: ignore
+args = {{envs.args | repr}}  # pyright: ignore
+
+if not is_valid_gs_file_url(url):
+    raise Exception(
+        f"Invalid Google Cloud Storage URL for a file: {url}. "
+        "URL should be in the format gs://bucket/path/to/file"
+    )
+
+if not is_logged_in(gcloud):
+    raise Exception(
+        "You need to be logged in to gcloud to download files. "
+        "Please run `gcloud auth login` first."
+    )
+
+args[""] = [gcloud, "storage", "cp", url, outfile]
+
+run_command(dict_to_cli_args(args, dashify=True), fg=True)

biopipen/scripts/web/gcloud_common.py

@@ -0,0 +1,49 @@
+"""Provides common functions for interacting with Google Cloud Storage."""
+from biopipen.utils.misc import run_command
+
+
+def is_logged_in(gcloud: str) -> bool:
+    """Check if the user is logged in to Google Cloud Storage.
+
+    Args:
+        gcloud: Path to the `gcloud` executable.
+
+    Returns:
+        bool: True if the user is logged in, False otherwise.
+    """
+    out = run_command([gcloud, "auth", "list"], stdout="RETURN")
+    return "ACTIVE" in out
+
+
+def is_valid_gs_bucket_url(url: str) -> bool:
+    """Check if a URL is a valid Google Cloud Storage bucket URL.
+
+    Such as `gs://bucket`.
+    """
+    if not url.startswith("gs://"):
+        return False
+
+    url = url.rstrip("/")
+    return "/" not in url[5:]
+
+
+def get_file_path(url: str) -> str:
+    """Get the file path from a Google Cloud Storage file URL, without bucket.
+
+    For example: gs://bucket/path/to/file -> path/to/file
+
+    Args:
+        url: The Google Cloud Storage file URL.
+
+    Returns:
+        str: The file path.
+    """
+    return url[5:].split("/", 1)[1]
+
+
+def is_valid_gs_file_url(url: str) -> bool:
+    """Check if a URL is a valid Google Cloud Storage file URL.
+
+    Such as `gs://bucket/path/to/file`.
+    """
+    return url.startswith("gs://")

{biopipen-0.29.2.dist-info → biopipen-0.31.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.29.2
+Version: 0.31.0
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -14,9 +14,9 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: runinfo
 Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
-Requires-Dist: pipen-board[report] (>=0.15,<0.16)
-Requires-Dist: pipen-cli-run (>=0.13,<0.14)
-Requires-Dist: pipen-filters (>=0.13,<0.14)
-Requires-Dist: pipen-poplog (>=0.1.2,<0.2.0)
-Requires-Dist: pipen-runinfo (>=0.6,<0.7) ; extra == "runinfo"
-Requires-Dist: pipen-verbose (>=0.11,<0.12)
+Requires-Dist: pipen-board[report] (>=0.16,<0.17)
+Requires-Dist: pipen-cli-run (>=0.14,<0.15)
+Requires-Dist: pipen-filters (>=0.14,<0.15)
+Requires-Dist: pipen-poplog (>=0.2.0,<0.3.0)
+Requires-Dist: pipen-runinfo (>=0.7,<0.8) ; extra == "runinfo"
+Requires-Dist: pipen-verbose (>=0.12,<0.13)

{biopipen-0.29.2.dist-info → biopipen-0.31.0.dist-info}/RECORD

@@ -1,9 +1,9 @@
-biopipen/__init__.py,sha256=f5--I8wu8KDVcUAUM1dKof58bj59kV6atq2ccm3sqPs,23
+biopipen/__init__.py,sha256=TJt1pYzTJuPE6GzDP1gxaeeVQlzcoUyEmSVSUPgYnIA,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
-biopipen/core/config.toml,sha256=IL31RfhuF-6V46lvLs1F-Z4SPmUuTvWzk5PN37Xjrqc,1907
+biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
-biopipen/core/filters.py,sha256=-OIzS5F_yNZ0Nk5Ci16BepPWqLOGBmYVqX3W98RSK9Y,12488
+biopipen/core/filters.py,sha256=5bZsbpdW7DCxqiteRdb2gelmXvfqWPmPsFxrpHdWsoE,12987
 biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
 biopipen/core/testing.py,sha256=lZ_R5ZbYPO2NPuLHdbzg6HbD_f4j8paVVbyeUqwg6FE,3411
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -18,17 +18,17 @@ biopipen/ns/delim.py,sha256=fejsh4KW1TG5oMZzAC238LvQhBz7brXkfl3BHfnLK5M,5612
 biopipen/ns/gene.py,sha256=rty-Bjcf87v2vyb9X4kRvfrQ6XQYXgN4f2ftFO0nWA8,3888
 biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
 biopipen/ns/misc.py,sha256=qXcm0RdR6W-xpYGgQn3v7JBeYRWwVm5gtgSj2tdVxx4,2935
-biopipen/ns/plot.py,sha256=r0n10N9iipZgbDZzkJVq4-9drMtinGK0ntBa3Lk2JFc,15771
+biopipen/ns/plot.py,sha256=_dGLKpyHiJqLIIQu5tqCk8H5BkgGBh_qRUZHkjnOgtE,18080
 biopipen/ns/regulatory.py,sha256=qvc9QrwgwCI_lg0DQ2QOZbAhC8BAD1qnQXSGtAGlVcY,11750
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=0MG0uyyrlSfjS-Lp2Abm_4f4LnLwyjUd6mIOtaQv36Q,108085
+biopipen/ns/scrna.py,sha256=fXP_h7gchcuk_Jwos0IgY_P8ON6Q995OgKHgdrxfvAY,112868
 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
 biopipen/ns/snp.py,sha256=-Jx5Hsv_7KV7TqLU0nHCaPkMEN0CFdi4tNVlyq0rUZ4,27259
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
 biopipen/ns/tcr.py,sha256=0PCF8iPZ629z6P3RHoAWEpMWmuDslomTGcMopjqvXmE,88304
 biopipen/ns/vcf.py,sha256=0aKH_YSLy_-JzV-_VZb0EoScv7JKGrDU7BaeWHjDuRo,22699
-biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
+biopipen/ns/web.py,sha256=4itJzaju8VBARIyZjDeh5rsVKpafFq_whixnvL8sXes,5368
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
 biopipen/reports/bam/CNVpytor.svelte,sha256=s03SlhbEPd8-_44Dy_cqE8FSErhUdqStLK39te5o7ZE,1364
 biopipen/reports/bam/ControlFREEC.svelte,sha256=OwN96RW0dN-gtQ1zWKbXYZCYkkrOC0RQmP3UG4x7zqU,837
@@ -76,7 +76,7 @@ biopipen/reports/vcf/TruvariBenchSummary.svelte,sha256=yew8HRN-YahBzX504Micah5BT
 biopipen/reports/vcf/TruvariConsistency.svelte,sha256=BBvtxi1EPmGH7j5M5zMOcLEhKWZOlKoXp1lrQGAmz_0,647
 biopipen/scripts/bam/BamMerge.py,sha256=jyaJI0-TulAxaCzvrYjC8PujH_ECNInevnPbh2_XQtU,3477
 biopipen/scripts/bam/BamSplitChroms.py,sha256=b7GS2I4X0dLOhlPg_r9-buoIHTWlq6zHI3Rox94LXR8,4893
-biopipen/scripts/bam/CNAClinic.R,sha256=EbQ1s1_y2uCERTP1aP0Fwu_dO4n8k1YSMBswwVs0uDQ,5040
+biopipen/scripts/bam/CNAClinic.R,sha256=mQXwtShL54HZXGCPqgPKPrU74_6K_8PqtOtG0mgA-F0,5062
 biopipen/scripts/bam/CNVpytor.py,sha256=hOUli9BDMOoth0or-tjUYC1AP3yNOuxUS6G3Rhcg99s,18000
 biopipen/scripts/bam/ControlFREEC.py,sha256=oX6iWsos-CfiT_ViDBrKeMOOIVdCKWrB-_MqzLgEF9s,3267
 biopipen/scripts/bed/Bed2Vcf.py,sha256=u0mp_2Y4UtEA839zq9UENesH6Gyiwd4sZQW9wFnBVU0,5090
@@ -84,11 +84,11 @@ biopipen/scripts/bed/BedConsensus.py,sha256=gfAxuIalvCEpS0tiOyAJGPYGgHN0L-hm0K37
 biopipen/scripts/bed/BedLiftOver.sh,sha256=Y4gBsz9w4zhE29UmWojO6F4PXMMMWC1uCzjrxa19eOs,256
 biopipen/scripts/bed/BedtoolsIntersect.py,sha256=sFyXPL3kG59xa5eJwHumcQLw3lfabOXsq2-k8IgIqt4,1722
 biopipen/scripts/bed/BedtoolsMerge.py,sha256=7mt307V_wWa_ME0VfuMsVX0HgEwfDcZtY_bDvOPjFiQ,368
-biopipen/scripts/cellranger/CellRangerCount.py,sha256=Mi6PiufFPp-cb4WRgZhniXi2ja5VUusRDW9RdAqFyX0,2831
-biopipen/scripts/cellranger/CellRangerSummary.R,sha256=8EqP4j074RLi5Adw47xyqQwkDEcvSS6Yfk0UgKKYOuo,11045
+biopipen/scripts/cellranger/CellRangerCount.py,sha256=b9kkHPpq-bFh-3XCUdxdMKg3SsZmEzZFrG3dbtb4fX8,2875
+biopipen/scripts/cellranger/CellRangerSummary.R,sha256=mVOCIHngEpJIKVD3tMG5UWqS0OQGGjY6yx6ikRcqQU4,11067
 biopipen/scripts/cellranger/CellRangerVdj.py,sha256=ipGkPzkiVy5IpPrYKUK4zgEIvz-aMJOKbMEN-bMStFE,2200
-biopipen/scripts/cnv/AneuploidyScore.R,sha256=OldqRUr4rn8AZZCLDaX5xCIR1e0R7XXb_RQ2hXDHHog,9142
-biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=fhffzQ5tW13KSgGz9CNDmvgqxUR1NDVVrsW_5xl1968,12410
+biopipen/scripts/cnv/AneuploidyScore.R,sha256=Bpm1cU7VkoinoKKzMuzqFntS8hjdd2IpBUjDiZyM7l4,9163
+biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=dSnekzXetM8BDmZPhHOS8WwEeOfszPfqthq6TrZ3aPc,12452
 biopipen/scripts/cnv/TMADScore.R,sha256=IH07REfBO3QB2QNWuwGY6LgAUAOE0lsfP6W0bS67zGs,1530
 biopipen/scripts/cnv/TMADScoreSummary.R,sha256=w58LD5xHnLal9jv53nBUGpQ8eTkAyEk1leCVN2T_ZaM,7109
 biopipen/scripts/cnvkit/CNVkitAccess.py,sha256=UerX66utY8UdlI1mlSVD7E9O0ByLnHzt6G3Urb8mCWE,689
@@ -104,23 +104,24 @@ biopipen/scripts/cnvkit/CNVkitReference.py,sha256=dO5vzqlgfecYUNJ3I2TvBdL_zKEJyK
 biopipen/scripts/cnvkit/CNVkitScatter.py,sha256=7DhTiXPHEHbdXn0VFcDOR-wTP6sks08N94KG7zjo_Is,2728
 biopipen/scripts/cnvkit/CNVkitSegment.py,sha256=q5iGAjY6-yIehPcJpi3hX6EuGre0YgWTPkG_d5LEV48,1629
 biopipen/scripts/cnvkit/guess_baits.py,sha256=7OCMtSMHIJWWZv9qEYVXnB0N4hU_JaGEesKdkr6tvJc,10586
-biopipen/scripts/delim/RowsBinder.R,sha256=yp960u7Ui_jFCL8WDvODa-0vhJvyLo64ll35PzXYUbI,1444
-biopipen/scripts/delim/SampleInfo.R,sha256=5NWYMIgeXjIwmIF-CTifUVyMLiy6RY_6xOMk2iG4v4E,6684
-biopipen/scripts/gene/GeneNameConversion.R,sha256=uAnueB1poicYpQHjUnl4ZBFn3sAWzP9HzmBC7zjlehI,1776
+biopipen/scripts/delim/RowsBinder.R,sha256=1QtRiPdUoxR8st1nxBMyVXgpcLfeF-iGsMYHz-66L2s,1465
+biopipen/scripts/delim/SampleInfo.R,sha256=xnpOGHGOMZeD_Ay7PBN9GkqW34sVkTufMIhbxKTw3wU,6727
+biopipen/scripts/gene/GeneNameConversion.R,sha256=Jy2ykhCj9ClSdQUfdYavh2LaBm0nOIXY2kJKmpsqOlI,1818
 biopipen/scripts/gene/GenePromoters.R,sha256=0ukq3-wpN6uq_cyJlQvKDVvy0Dv8cI5Htd9t2xpkEyk,2021
-biopipen/scripts/gsea/Enrichr.R,sha256=tr4vInlVIeiGXumh22ARuTQmy0-Qq869RiX7d7ERqCg,661
-biopipen/scripts/gsea/FGSEA.R,sha256=RLqDgrqnYEacHfzEEuZ3d29lxNqWehigOnGuu248SRg,1483
-biopipen/scripts/gsea/GSEA.R,sha256=gkiigYQ9xNdqZWMus0h0htSdWWbLJt9uXPo8Bc4hOaI,1083
-biopipen/scripts/gsea/PreRank.R,sha256=onZK1FQa6yDO0Fz4juy56XQjpzyw3zBdZv7edY9acNI,1356
+biopipen/scripts/gsea/Enrichr.R,sha256=gqN93oE3OeqW_TXZiE_gNH89_o_XFwnOWcHxhTUMvNs,724
+biopipen/scripts/gsea/FGSEA.R,sha256=KpZWM-oskitRaMBDoXQoxa3zcSjZnN-fosKrzEgX28c,1525
+biopipen/scripts/gsea/GSEA.R,sha256=Qo-QUY4B539Hm2FbsS2lsfgAxP_2FrhtPUN1Feq1Jmc,1125
+biopipen/scripts/gsea/PreRank.R,sha256=qrqaf_0ghgpaS3d9XbNVCZS7ZEbZaEoxNzTQ2zkVB_Y,1398
 biopipen/scripts/misc/Config2File.py,sha256=NUio0uOEuZtUBpuByDSItYu9Kwu5mosb4pdPq5-QAmE,440
 biopipen/scripts/misc/Shell.sh,sha256=Rg8_DOfDFeUjZ_1_EVm2lbzyMLqcEv9A3k6SsTcfZZ0,493
 biopipen/scripts/misc/Str2File.py,sha256=99oQNxChxChNJ9vmD77b48cu-r_P_heSpx7A5wi3qTE,212
-biopipen/scripts/plot/Heatmap.R,sha256=4v_oRME8ZiwczIlBIp-OP_YPWLAvBKzbHiwNBCZ0Xog,1982
-biopipen/scripts/plot/Manhattan.R,sha256=QJhJ80d0RycRt26zJXDqkuCh88YW5IkD-8Di2lGSeu8,4732
-biopipen/scripts/plot/QQPlot.R,sha256=HHGBEJKwHz0ZsYdmAebwov9gQuf6taaLTRkeO7KJ8Lw,4094
-biopipen/scripts/plot/ROC.R,sha256=Cr-mHQx6c748fQYkOWO2xIKWwiVAUxGuxn6lYEhNH78,2430
-biopipen/scripts/plot/VennDiagram.R,sha256=GVc-kyHqnXrbXZvy-evcxI1XGtlLSChBiVnMjPywNMA,731
-biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=eeBauaAfyEcOIznoXRRWXeRUvAd0waU0R5CCzwQ8kgs,8969
+biopipen/scripts/plot/Heatmap.R,sha256=xD_X-0J3kVdKPctTUGeBFXxNgd6N6XbBfBb3giFePJU,2045
+biopipen/scripts/plot/Manhattan.R,sha256=7lJwCX1d0zUpJVhVcmQ35ZtQELzkaDNnBTNHHc3cxW0,4754
+biopipen/scripts/plot/QQPlot.R,sha256=Xil19FJ7jbsxo1yU7dBhhZo2_95Gz6gpTyuv9F0RDNM,4115
+biopipen/scripts/plot/ROC.R,sha256=cjmmYRQycYisqRmlkZE9nbmwfo-04wdJKVmlOsiEFAM,2451
+biopipen/scripts/plot/Scatter.R,sha256=fg4H5rgdr6IePTMAIysiElnZme0vCh1T0wrwH2Q9xkM,2840
+biopipen/scripts/plot/VennDiagram.R,sha256=IQG4OLXdORbmKMWca7dtSDX_RdH8FCrpDfi3eMae7G8,773
+biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=1sR3sWRZbxDeFO290LcpzZglzOLc13SSvibDON96PCg,8852
 biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R,sha256=SAyTm2-6g5qVJFRrLxEY0QJrLWTkwDi_J_9J7HhtTN8,4438
 biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R,sha256=wCK4tLx1iWh_OwW7ZvLTCjTGWCIfVqw-lYC0-JqIPqg,3338
 biopipen/scripts/regulatory/MotifScan.py,sha256=WtSbs8z08oeTgzjr0LfIDmjbUdknAh1raa_QPQ_NCFg,5336
@@ -128,99 +129,105 @@ biopipen/scripts/regulatory/atSNP.R,sha256=TXJARbE0rDIzSq6Spacz_HsM_DXdREJ95ZsBg
 biopipen/scripts/regulatory/motifBreakR.R,sha256=trzvvTvwc5gSO427wkqx93FecuQxLGa9kNqodKa8S0U,70236
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 biopipen/scripts/tcr/TCRDock.py,sha256=jjzxMWp-hs0LDtA1mVbiWDvUieSO7X-F9yeKGy1LSTM,3026
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 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
 biopipen/scripts/tcr/TESSA_source/BriseisEncoder.py,sha256=z4_Q_6StymffuUGGjHP1-B3aTsXtamKao5Q1-Kg9has,6831
 biopipen/scripts/tcr/TESSA_source/MCMC_control.R,sha256=93Nnz0IG8KfFnVscZDvmBp1qccZoSoG_jIVpOWBQLHE,2911
@@ -239,8 +246,8 @@ biopipen/scripts/vcf/BcftoolsFilter.py,sha256=AdQMXFTNLCS5eqYWMNIMbkK8qXJ5j8GYm7
 biopipen/scripts/vcf/BcftoolsSort.py,sha256=tU0pTrEIB-7x6iOSfU-KpYY1rEidi6Q4179NntY3cGc,3778
 biopipen/scripts/vcf/BcftoolsView.py,sha256=Sj3KkYPpwQFo5kmZC5MRxItrSE5KVZi0jNYrRFck3Ow,2465
 biopipen/scripts/vcf/TruvariBench.sh,sha256=80yLQ73OzSgsJ4ltzgpcWxYvvX1hFnCG8YSBhhhRQ9Y,765
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 biopipen/scripts/vcf/Vcf2Bed.py,sha256=LzyJ9qW1s5mbfF8maLc77_0rE98KMc2lq1R94_NFbSU,855
 biopipen/scripts/vcf/VcfAnno.py,sha256=FW626rAs_WSU7AHQMKjfkYoByUGh_gVyJM97neGfOMo,802
 biopipen/scripts/vcf/VcfDownSample.sh,sha256=yBlyoA8xyHPkVc1XAs1biNZmN7rDR-CMz8qVh2GGvuk,939
@@ -254,6 +261,9 @@ biopipen/scripts/vcf/VcfSplitSamples.py,sha256=GraKi7WluzDAvVVGljwd3Yif6MriniF8s
 biopipen/scripts/vcf/bcftools_utils.py,sha256=p91rZp0RG6AtbpYA_KuKCfa6T5aNKMq_rK95QPL7mMI,1514
 biopipen/scripts/web/Download.py,sha256=WKC_t5ZEeJoKFyY9XwksHARcMbKmHMcxNEUDLMGJ0Cc,924
 biopipen/scripts/web/DownloadList.py,sha256=cZvdi3LVzlATiTvAXe0uuDDXGqB5jcR2zHrMLCEb2U8,1130
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 biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biopipen/utils/common_docstrs.py,sha256=Ow-g-yS5P7DEO37cP1X-xioRbYWygfQHxIuLIaDdrjs,6288
@@ -269,7 +279,7 @@ biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5
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 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
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