biopipen 0.23.7__py3-none-any.whl → 0.24.0__py3-none-any.whl

biopipen/scripts/tcr/TESSA.R

@@ -134,7 +134,9 @@ if (has_VJ) {
         file.path(tessa_dir, "tcr_vj.txt")
     )
 }
-log_info(paste("- ", cmd_encoder))
+print("Running:")
+print(cmd_encoder)
+log_debug(paste("- ", cmd_encoder))
 
 rc <- system(cmd_encoder)
 if (rc != 0) {

biopipen/scripts/tcr/immunarch-patched.R

@@ -0,0 +1,142 @@
+library(immunarch)
+
+vis.immunr_gini <- function(.data, .by = NA, .meta = NA,
+                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
+                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5,
+                            .legend = NA, .plot.type = "bar", ...) {
+  # repDiversity(..., .method = "gini") generates a matrix
+  .data = data.frame(Sample = rownames(.data), Value = .data[, 1])
+  if (.plot.type == "bar") {
+    vis_bar(
+        .data = .data, .by = .by, .meta = .meta,
+        .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
+        .points = .points, .test = .test, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, "Gini coefficient"),
+        .title = "Gini coefficient", .subtitle = "Sample diversity estimation using the Gini coefficient",
+        .legend = .legend, .leg.title = NA
+    )
+  } else {
+    vis_box(
+        .data = .data, .by = .by, .meta = .meta, .test = .test,
+        .points = .points, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, "Gini coefficient"),
+        .title = "Gini coefficient", .subtitle = "Sample diversity estimation using the Gini coefficient",
+        .legend = .legend, .leg.title = NA, .melt = FALSE
+    )
+  }
+}
+
+vis.immunr_div <- function(.data, .by = NA, .meta = NA,
+                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
+                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5,
+                            .legend = NA, .plot.type = "bar", ...) {
+  # repDiversity(..., .method = "gini") generates a matrix
+  if (.plot.type == "bar") {
+    immunarch:::vis.immunr_div(.data = .data,.by = .by, .meta = .meta,
+        .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
+        .points = .points, .test = .test, .signif.label.size = .signif.label.size,
+        .legend = .legend)
+  } else {
+    vis_box(
+        .data = .data, .by = .by, .meta = .meta, .test = .test,
+        .points = .points, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, "Effective number of clonoypes"),
+        .title = "True diversity", .subtitle = "Sample diversity estimation using the true diversity index",
+        .legend = NA, .leg.title = NA, .melt = FALSE
+    )
+  }
+}
+
+vis.immunr_chao1 <- function(.data, .by = NA, .meta = NA,
+                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
+                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5,
+                            .legend = NA, .plot.type = "bar", ...) {
+  # repDiversity(..., .method = "gini") generates a matrix
+  if (.plot.type == "bar") {
+    immunarch:::vis.immunr_chao1(.data = .data,.by = .by, .meta = .meta,
+        .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
+        .points = .points, .test = .test, .signif.label.size = .signif.label.size,
+        .legend = .legend)
+  } else {
+    .data <- data.frame(Sample = row.names(.data), Value = .data[, 1])
+    vis_box(
+        .data = .data, .by = .by, .meta = .meta, .test = .test,
+        .points = .points, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, "Chao1"),
+        .title = "Chao1", .subtitle = "Sample diversity estimation using Chao1",
+        .legend = NA, .leg.title = NA, .melt = FALSE
+    )
+  }
+}
+
+vis.immunr_ginisimp <- function(.data, .by = NA, .meta = NA,
+                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
+                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5,
+                            .legend = NA, .plot.type = "bar", ...) {
+  # repDiversity(..., .method = "gini") generates a matrix
+  if (.plot.type == "bar") {
+    immunarch:::vis.immunr_ginisimp(.data = .data,.by = .by, .meta = .meta,
+        .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
+        .points = .points, .test = .test, .signif.label.size = .signif.label.size,
+        .legend = .legend)
+  } else {
+    vis_box(
+        .data = .data, .by = .by, .meta = .meta, .test = .test,
+        .points = .points, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, "Gini-Simpson index"),
+        .title = "Gini-Simpson index", .subtitle = "Sample diversity estimation using the Gini-Simpson index",
+        .legend = .legend, .leg.title = NA, .melt = FALSE
+    )
+  }
+}
+
+vis.immunr_invsimp <- function(.data, .by = NA, .meta = NA,
+                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
+                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5,
+                            .legend = NA, .plot.type = "bar", ...) {
+  # repDiversity(..., .method = "gini") generates a matrix
+  if (.plot.type == "bar") {
+    immunarch:::vis.immunr_invsimp(.data = .data,.by = .by, .meta = .meta,
+        .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
+        .points = .points, .test = .test, .signif.label.size = .signif.label.size,
+        .legend = .legend)
+  } else {
+    vis_box(
+        .data = .data, .by = .by, .meta = .meta, .test = .test,
+        .points = .points, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, "Inverse Simpson index"),
+        .title = "Inverse Simpson index", .subtitle = "Sample diversity estimation using the inverse Simpson index",
+        .legend = .legend, .leg.title = NA, .melt = FALSE
+    )
+  }
+}
+
+vis.immunr_dxx <- function(.data, .by = NA, .meta = NA,
+                            .errorbars = c(0.025, 0.975), .errorbars.off = FALSE,
+                            .points = TRUE, .test = TRUE, .signif.label.size = 3.5,
+                            .legend = NA, .plot.type = "bar", ...) {
+  # repDiversity(..., .method = "gini") generates a matrix
+  if (.plot.type == "bar") {
+    immunarch:::vis.immunr_dxx(.data = .data,.by = .by, .meta = .meta,
+        .errorbars = .errorbars, .errorbars.off = .errorbars.off, .stack = FALSE,
+        .points = .points, .test = .test, .signif.label.size = .signif.label.size,
+        .legend = .legend)
+  } else {
+    perc_value <- round(.data[1, 2][1])
+    .data <- data.frame(Sample = row.names(.data), Value = .data[, 1])
+    vis_box(
+        .data = .data, .by = .by, .meta = .meta, .test = .test,
+        .points = .points, .signif.label.size = .signif.label.size,
+        .defgroupby = "Sample", .grouping.var = "Group",
+        .labs = c(NA, paste0("D", perc_value)),
+        .title = paste0("D", perc_value, " diversity index"), .subtitle = paste0("Number of clonotypes occupying the ", perc_value, "% of repertoires"),
+        .legend = .legend, .leg.title = NA, .melt = FALSE
+    )
+  }
+}

biopipen/utils/caching.R

@@ -0,0 +1,44 @@
+library(digest)
+
+#' Get signatures and cached data
+#'
+#' @param x An object to infer signature from
+#' @param kind A string indicating the kind of the object
+#'   Used as part of the filename of the cached file
+#' @param cache_dir A string indicating the directory to store cached files
+#'
+#' @return A list containing the signature, digested signature and cached data
+get_cached <- function(x, kind, cache_dir) {
+    if (is.null(cache_dir) || isFALSE(cache_dir)) {
+        return(list(sig = NULL, dig = NULL, data = NULL))
+    }
+    # Get signature of an object
+    sig <- capture.output(str(x))
+    dig <- digest::digest(sig, algo = "md5")
+    dig <- substr(dig, 1, 8)
+    cached_file <- file.path(cache_dir, paste0(dig, ".", kind, ".RDS"))
+    if (!file.exists(cached_file)) {
+        return(list(sig = sig, dig = dig, data = NULL))
+    }
+
+    list(sig = sig, dig = dig, data = readRDS(cached_file))
+}
+
+#' Save an object to cache
+#'
+#' @param to_cache An list to cache,
+#'   including the signature, digested signature and data
+#' @param kind A string indicating the kind of the object
+#'   Used as part of the filename of the cached file
+#' @param cache_dir A string indicating the directory to store cached files
+save_to_cache <- function(to_cache, kind, cache_dir) {
+    if (is.null(cache_dir) || isFALSE(cache_dir)) { return() }
+    dig <- to_cache$dig
+    sig <- to_cache$sig
+    data <- to_cache$data
+    # Save an object to cache
+    sig_file <- file.path(cache_dir, paste0(dig, ".", kind , ".signature.txt"))
+    writeLines(c(as.character(Sys.time()), "", sig), sig_file)
+    cached_file <- file.path(cache_dir, paste0(dig, ".", kind, ".RDS"))
+    saveRDS(data, cached_file)
+}

{biopipen-0.23.7.dist-info → biopipen-0.24.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.23.7
+Version: 0.24.0
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -14,9 +14,10 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: runinfo
-Requires-Dist: datar[pandas] (>=0.15.2,<0.16.0)
-Requires-Dist: pipen-board[report] (>=0.13,<0.14)
-Requires-Dist: pipen-cli-run (>=0.11,<0.12)
-Requires-Dist: pipen-filters (>=0.10,<0.11)
-Requires-Dist: pipen-runinfo (>=0.4,<0.5) ; extra == "runinfo"
-Requires-Dist: pipen-verbose (>=0.9,<0.10)
+Requires-Dist: datar[pandas] (>=0.15.3,<0.16.0)
+Requires-Dist: pipen-board[report] (>=0.14,<0.15)
+Requires-Dist: pipen-cli-run (>=0.12,<0.13)
+Requires-Dist: pipen-filters (>=0.11,<0.12)
+Requires-Dist: pipen-poplog (>=0.0.2,<0.0.3)
+Requires-Dist: pipen-runinfo (>=0.5,<0.6) ; extra == "runinfo"
+Requires-Dist: pipen-verbose (>=0.10,<0.11)

{biopipen-0.23.7.dist-info → biopipen-0.24.0.dist-info}/RECORD

@@ -1,16 +1,16 @@
-biopipen/__init__.py,sha256=cC_HEsX6d06QmpjNLfRezzJvL501PPwiQYXWDM2_2UI,23
+biopipen/__init__.py,sha256=DxtMZD542lg_xb6icrE2d5JOY8oUi-v34i2Ar63ddvs,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=Rn7Cta7WsMtmQkKGC4h9d5dU_STaIVBgR8UliiGgL6o,1757
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
 biopipen/core/filters.py,sha256=HLrjXGsvvjRtTWIAmg_f4IMymWaRD769HlDwsCTh170,12424
-biopipen/core/proc.py,sha256=7TsjBM7EEtMMB-w4jbxV_CSRY8J970gM8320Ga1YeHU,717
+biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
 biopipen/core/testing.py,sha256=5vR15kkCjfXM7Bx0HBzabNLtDLAEX4uU94TskCkPni8,1447
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/ns/bam.py,sha256=5AsYrB0mtr_mH6mCL6gjJ5rC4NywpjFkpFjUrBGp7Fk,9301
 biopipen/ns/bcftools.py,sha256=puCDfIL-1z6cz2y1Rlz-ESNIr8xJgeIjEQ440qicCvM,3467
 biopipen/ns/bed.py,sha256=UN38qUChDeE-ipuSBY8RVLwvJqM2wxSRmlhOiDo4JG0,5395
-biopipen/ns/cellranger.py,sha256=0A6pCpBLg1zKm2Ve2cXvGvNNK4lMqdsek2iTer5X_TI,3679
+biopipen/ns/cellranger.py,sha256=vwyPNaiRIFMp1e8kSJ1UNsE9ZcUykNniakKE-BqZR60,3681
 biopipen/ns/cnv.py,sha256=vq6dZfEOyuVuqg3nP6FQtNmQ-JocpBJMX9IYlZ0OPD0,6803
 biopipen/ns/cnvkit.py,sha256=5mA2Q8-YDs4g1HoxtpB_NWnyZYwEThNr3s3wlubLQrQ,31130
 biopipen/ns/cnvkit_pipeline.py,sha256=2fJLn70L2jJ81ZMNdnU84Sf3HoKA2CSnHuDzLGR8jmw,36854
@@ -20,10 +20,10 @@ biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
 biopipen/ns/misc.py,sha256=fzn0pXvdghMkQhu-e3MMapPNMyO6IAJbtTzVU3GbFa0,3246
 biopipen/ns/plot.py,sha256=yguxmErUOH-hOM10JfuI_sXw2p49XF8yGR_gXfbd5yQ,4066
 biopipen/ns/rnaseq.py,sha256=l4vFeRasGhkexopGTM_VfSyIFewOxg-9L5niFzhWUNA,565
-biopipen/ns/scrna.py,sha256=42cM6n7rNy8sze9Lhl90RNkpxWT5w6LKPDrGsAK_Y7U,95808
+biopipen/ns/scrna.py,sha256=A3OcbCQzbOanPqn7_ZVeGvMpTAPDM24KM8ZFUUsWs6g,95467
 biopipen/ns/scrna_metabolic_landscape.py,sha256=9s1NvH3aMaNDXyfwy9TdzGcSP_lIW4JqhLgknNZcIKE,28313
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=IcP1uD8U9XD6UbOgdjA_Lk5PK6r4R84Gi7511uvXoy8,84411
+biopipen/ns/tcr.py,sha256=Pl6flJsgzcjExc3x9Eg_uiNkQprqmUTqKtmImM66zNY,84411
 biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
 biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
@@ -124,29 +124,29 @@ biopipen/scripts/scrna/MetaMarkers.R,sha256=kgjk65EmewZ1uh8AoiENDLmNFe4lzmYvssJe
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=JSHd-_-KiFqW8avCGxgU4T-C5BtDr2u0kwIvEu2lFIg,4188
 biopipen/scripts/scrna/RadarPlots.R,sha256=iR4JKtO2b3hGfqv_KAI7BR9tq02EAYfKeqp7tzAicKs,14808
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
-biopipen/scripts/scrna/ScFGSEA.R,sha256=2nJN1AAe55SyR-jwVj5ds2pyt32fTIn548zjvEB4Jt0,7332
+biopipen/scripts/scrna/ScFGSEA.R,sha256=E6Rx-0TjplP_nptDCE-LqMyipsOFaMU3hM7FjjFFFDY,7538
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=pZKv1SnSNEGXDeE0_2VYp0GAikYitohW2FR5YGKjs8Q,2351
 biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=SaKTJloP1fttRXZQeb2ApX0ej7al13wOoEYkthSk13k,15489
 biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=GTZfs1yOkuoMUM1Zb19i_My8B8b1Qtve8je55pU_w-g,5054
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=GVKIXFNS_syCuSN8oxoBkjxxAeI5LdSxh-qLVkUsbDA,2146
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=CE9989SaO75_KYEEVqivEbUoTcUOtiTkRGWLNtWzxI8,6450
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=PeXa3r2VTo0Q1rdXpSfAOIbYSJAcA8WUNM-tJkNUcPg,1284
-biopipen/scripts/scrna/SeuratClustering.R,sha256=Q3XGg0Rq1xqswyQSsj8AmarmiT9ZFdoolXy2g9ibiTo,5185
+biopipen/scripts/scrna/SeuratClustering.R,sha256=kAvQq3RV86_KSv9NlUtUeQrPKkbhSsnv6Q4DoiTu8M0,6403
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
 biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=tisYmoSaCX8Kl8y6euuuUroWdDsJ2NGI27J5AWr9Niw,4392
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=Pp4GsF3hZ6ZC2vroC3LSBmVa4B1p2L3hbh981yaAIeQ,1093
-biopipen/scripts/scrna/SeuratPreparing.R,sha256=3X2-yCjNdYVMFNozRU38RxhNBOL-lPo9Za1qUT7V5wI,12227
+biopipen/scripts/scrna/SeuratPreparing.R,sha256=KNrBPibqANhCsCctOGCOMPLTjDDd-iDRpMSCXkPuUQU,12994
 biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0hTiSvsU,754
-biopipen/scripts/scrna/SeuratSubClustering.R,sha256=6b1J98YYK2gwJ_qkpuvYIdlj6uWxJA8IpUXvaCjgC_U,6334
+biopipen/scripts/scrna/SeuratSubClustering.R,sha256=L1SwKhNNKvsQGrcj0ZjScW9BLuvdO2pg7U48Ospsot8,6096
 biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi5epO6SKM,1776
 biopipen/scripts/scrna/SeuratTo10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5wshqY,2679
 biopipen/scripts/scrna/TopExpressingGenes.R,sha256=m1BEpDfrzD9rJ2wEwA355GMqBq8Wfc_PzCjtLavB68Q,7754
 biopipen/scripts/scrna/Write10X.R,sha256=OMhXvJwvaH-aWsMpijKrvXQVabc1qUu5ZEwiLAhkDeY,285
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
 biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=UbNoyspFB8166VgbkkFyTS6tkA-7ybylfvO50eqNnBU,4841
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=dpyzIZU78zLHPLIEg9mAz8mK4XazxVuUm2CN33HGPpw,5233
-biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=_iTOOByaaXyolMN8_IMY2qcEcC_EAZGCPoHyrOqiTKI,16245
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=Kv69CkVm67K3w5EEcPQr7SlaWFpPwqTI0DVSUn62Rj0,5230
+biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=95DLX1Rz0tobOuDZ8V9YdGgO0KiNthhccoeeOK21tno,16216
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=0MIRrUjCtTDkUiL6GfKbtjC7bLlt50AGWFv4fl4e72k,9856
 biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
 biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
@@ -159,24 +159,24 @@ biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_Dg
 biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=Z7Q3cUr1Pvmy4CFADN0P7i9g1-HbzWROMqk5HvL_F1Q,45762
 biopipen/scripts/tcr/GIANA/Imgt_Human_TRBV.fasta,sha256=XUwDPXJxVH5O9Q0gCL6EILKXEwVyiAZXm4VS2vkPcnQ,15371
 biopipen/scripts/tcr/GIANA/query.py,sha256=5NWSEDNrJomMt48tzLGpRwJTZB0zQxvMVTilyG8osX8,7298
-biopipen/scripts/tcr/Immunarch-basic.R,sha256=lPmh8Il3bEvOHEpb4FN4BokRsq6cS2h47cT15YBv6fg,3194
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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
@@ -188,6 +188,7 @@ biopipen/scripts/tcr/TESSA_source/real_data.R,sha256=tg3BbiTpRVQWBRZStnzkC2jI1PC
 biopipen/scripts/tcr/TESSA_source/update.R,sha256=kVrf6zgIkhhiQ2O55XGmxm_DGBKSpcShFgkyPNQIet0,6661
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 biopipen/scripts/tcr/VJUsage.R,sha256=LjHEbAHW3WriCYiM9-T6Esd4jc6pnoiSxBKTN_YA490,437
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 biopipen/scripts/tcr/vdjtools-patch.sh,sha256=rL5qp2S18CrpqduKkeR1HVmmuWhCVJOMKJXvWiKdYIc,566
 biopipen/scripts/vcf/TruvariBench.sh,sha256=80yLQ73OzSgsJ4ltzgpcWxYvvX1hFnCG8YSBhhhRQ9Y,765
 biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=YlcD9qLtK3aeW3XeLx8pXTe7yOkbaYJyLHb2TYijm8A,1474
@@ -205,6 +206,7 @@ biopipen/scripts/vcf/VcfSplitSamples.py,sha256=GraKi7WluzDAvVVGljwd3Yif6MriniF8s
 biopipen/scripts/web/Download.py,sha256=WKC_t5ZEeJoKFyY9XwksHARcMbKmHMcxNEUDLMGJ0Cc,924
 biopipen/scripts/web/DownloadList.py,sha256=cZvdi3LVzlATiTvAXe0uuDDXGqB5jcR2zHrMLCEb2U8,1130
 biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biopipen/utils/common_docstrs.py,sha256=ro9dUXeHMXBaqb-hTafwrG6xW5IOBEeiUM2_REjFoCo,5842
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 biopipen/utils/gene.py,sha256=qE_BqTayrJWxRdniffhcz6OhZcw9GUoOrj2EtFWH9Gw,2246
@@ -218,7 +220,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
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 biopipen/utils/single_cell.R,sha256=bKduqOQjSC8BtZJuwfUShR49omoEMbB57n3Gi6dYlqA,4147
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
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