biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/scripts/cnv/TMADScoreSummary.R

@@ -1,9 +1,7 @@
-library(ggplot2)
-library(ggprism)
 library(dplyr)
 library(tidyr)
 library(tibble)
-library(patchwork)
+library(plotthis)
 
 tmadfiles = {{in.tmadfiles | r}}
 metafile  = {{in.metafile | r}}
@@ -47,10 +45,14 @@ if (!is.null(group_cols)) {
 }
 
 data = data.frame(Sample = sams, tMAD = tmads)
-if (file.exists(metafile) && length(meta_cols) > 0) {
+if (is.character(metafile) && file.exists(metafile) && length(meta_cols) > 0) {
     metadf = read.table(metafile, header=T, row.names=NULL, sep="\t", stringsAsFactors=F)
-    sample_col = colnames(metadf)[1]
-    meta = metadf[, c(sample_col, meta_cols), drop=FALSE]
+    if (!is.null(metadf$Sample)) {
+        metadf$Sample = as.character(metadf$Sample)
+    } else {
+        colnames(metadf)[1] = "Sample"
+    }
+    meta = metadf[, c("Sample", meta_cols), drop=FALSE]
     colnames(meta) = c("Sample", meta_cols)
     data = data %>% left_join(meta, by="Sample")
 }
@@ -59,20 +61,12 @@ if (file.exists(metafile) && length(meta_cols) > 0) {
 write.table(data, file=file.path(outdir, "tMAD.txt"), sep="\t", quote=F, row.names=F)
 
 # bar plot for all samples without grouping
-p = ggplot(data, aes(x=Sample, y=tMAD)) +
-    geom_bar(stat="identity", fill="steelblue") +
-    theme_prism() +
-    theme(
-        axis.text.x = element_text(angle=90, hjust=1, vjust=0.5),
-        axis.title.x = element_blank(),
-        axis.title.y = element_text(size=12),
-        axis.text.y = element_text(size=12),
-        legend.position = "none",
-    ) +
-    labs(
-        x = NULL,
-        y = "tMAD",
-    )
+p <- BarPlot(
+    data = data,
+    x = "Sample",
+    y = "tMAD",
+    x_text_angle = 90
+)
 
 png(file.path(outdir, "tMAD.png"), width=400 + length(sams) * 12, height=800, res=100)
 print(p)
@@ -84,41 +78,30 @@ if (!is.null(group_cols)) {
         if (!grepl(",", group_col, fixed = TRUE)) {
             # Bar plot with this group_col, but with different fill colors
             # for each group, and samples from the same group are next to each other
-            p = ggplot(
-                    data %>% arrange(!!sym(group_col)) %>% mutate(Sample=factor(Sample, levels=Sample)),
-                    aes(x=Sample, y=tMAD, fill=!!sym(group_col))
-                ) +
-                geom_bar(stat="identity") +
-                theme_prism() +
-                theme(
-                    axis.text.x = element_text(angle=90, hjust=1, vjust=0.5),
-                    axis.title.x = element_blank(),
-                    axis.title.y = element_text(size=12),
-                    axis.text.y = element_text(size=12),
-                ) +
-                labs(
-                    x = NULL,
-                    y = "tMAD",
-                )
+            gdata <- data %>% arrange(!!sym(group_col)) %>% mutate(Sample=factor(Sample, levels=unique(Sample)))
+            p <- BarPlot(
+                data = gdata,
+                x = "Sample",
+                y = "tMAD",
+                fill = group_col,
+                x_text_angle = 90
+            )
 
             png(file.path(outdir, paste0("tMAD_", group_col, "_bar.png")), width=400 + length(sams) * 12, height=600, res=100)
             print(p)
             dev.off()
 
             # Box plot overlays with violin plot with this group_col
-            p = ggplot(data, aes(x=!!sym(group_col), y=tMAD)) +
-                geom_boxplot(outlier.shape=NA, fill="white", color="black") +
-                geom_violin(fill="steelblue", alpha=0.5) +
-                theme_prism() +
-                theme(
-                    axis.title.x = element_text(size=12),
-                    axis.title.y = element_text(size=12),
-                    axis.text.y = element_text(size=12),
-                ) +
-                labs(
-                    x = group_col,
-                    y = "tMAD",
-                )
+            p <- ViolinPlot(
+                data = gdata,
+                x = group_col,
+                y = "tMAD",
+                x_text_angle = 90,
+                add_box = TRUE,
+                add_point = TRUE,
+                comparisons = TRUE,
+                sig_label = "p.format"
+            )
 
             png(file.path(outdir, paste0("tMAD_", group_col, "_box_violin.png")), width=1000, height=600, res=100)
             print(p)
@@ -133,25 +116,17 @@ if (!is.null(group_cols)) {
             # concatenate them together using patch work, with ncol=2
             # calcuate the height and width of the plot based on the number of
             # groups
-            ps = data %>%
-                group_by(!!sym(group_col1)) %>%
-                group_map(function(.x, .y) {
-                    p = ggplot(
-                            .x %>% arrange(!!sym(group_col2)) %>% mutate(Sample=factor(Sample, levels=Sample)),
-                            aes(x=Sample, y=tMAD, fill=!!sym(group_col2))
-                        ) +
-                        geom_bar(stat="identity") +
-                        theme_prism() +
-                        theme(
-                            axis.text.x = element_text(angle=90, hjust=1, vjust=0.5),
-                            axis.title.x = element_blank(),
-                            axis.title.y = element_text(size=12),
-                            axis.text.y = element_text(size=12),
-                        ) +
-                        labs(x = NULL, y = "tMAD") +
-                        ggtitle(.y[[group_col1]][1])
-                    p
-                })
+            gdata <- data %>% arrange(!!sym(group_col1), !!sym(group_col2)) %>%
+                mutate(Sample=factor(Sample, levels=unique(Sample)))
+            p <- BarPlot(
+                data = gdata,
+                x = "Sample",
+                y = "tMAD",
+                split_by = group_col1,
+                fill = group_col2,
+                x_text_angle = 90,
+                ncol = 2
+            )
 
             png(
                 file.path(outdir, paste0("tMAD_", group_col, "_bar.png")),
@@ -159,26 +134,22 @@ if (!is.null(group_cols)) {
                 height=length(unique(data[[group_col1]])) * 200,
                 res=100
             )
-            print(wrap_plots(ps, ncol=2))
+            print(p)
             dev.off()
 
             # Do the same for Voilin + boxplot
-            ps = data %>%
-                group_by(!!sym(group_col1)) %>%
-                group_map(function(.x, .y) {
-                    p = ggplot(.x, aes(x=!!sym(group_col2), y=tMAD)) +
-                        geom_boxplot(outlier.shape=NA, fill="white", color="black") +
-                        geom_violin(fill="steelblue", alpha=0.5) +
-                        theme_prism() +
-                        theme(
-                            axis.title.x = element_text(size=12),
-                            axis.title.y = element_text(size=12),
-                            axis.text.y = element_text(size=12),
-                        ) +
-                        labs(x = group_col2, y = "tMAD") +
-                        ggtitle(.y[[group_col1]][1])
-                    p
-                })
+            p <- ViolinPlot(
+                data = gdata,
+                x = group_col2,
+                y = "tMAD",
+                split_by = group_col1,
+                x_text_angle = 90,
+                add_box = TRUE,
+                add_point = TRUE,
+                comparisons = TRUE,
+                sig_label = "p.format",
+                ncol = 2
+            )
 
             png(
                 file.path(outdir, paste0("tMAD_", group_col, "_box_violin.png")),
@@ -186,7 +157,7 @@ if (!is.null(group_cols)) {
                 height=length(unique(data[[group_col1]])) * 200,
                 res=100
             )
-            print(wrap_plots(ps, ncol=2))
+            print(p)
             dev.off()
         }
     }

biopipen/scripts/cnvkit/CNVkitAccess.py

@@ -1,10 +1,11 @@
+from pathlib import Path, PosixPath  # noqa: F401
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-excfiles = {{in.excfiles | repr}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
-reffile = {{envs.ref | quote}}  # pyright: ignore
-cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
-min_gap_size = {{envs.min_gap_size | quote}}  # pyright: ignore
+excfiles: list[Path] = {{in.excfiles | each: as_path}}  # pyright: ignore # noqa
+outfile: str = {{out.outfile | quote}}  # pyright: ignore
+reffile: str = {{envs.ref | quote}}  # pyright: ignore
+cnvkit: str = {{envs.cnvkit | quote}}  # pyright: ignore
+min_gap_size: str = {{envs.min_gap_size | quote}}  # pyright: ignore
 
 
 def main():
@@ -12,7 +13,7 @@ def main():
         "": [cnvkit, "access"],
         "s": min_gap_size,
         "o": outfile,
-        "_": reffile,
+        "_": Path(reffile).expanduser(),
     }
     if excfiles:
         other_args["exclude"] = excfiles

biopipen/scripts/cnvkit/CNVkitAutobin.py

@@ -1,26 +1,34 @@
+from __future__ import annotations
+
+from pathlib import Path, PosixPath  # noqa: F401
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-bamfiles = {{in.bamfiles | repr}}  # pyright: ignore
-accfile = {{in.accfile | quote}}  # pyright: ignore
-baitfile = {{in.baitfile | repr}}  # pyright: ignore
-target_file = {{out.target_file | quote}}  # pyright: ignore
-antitarget_file = {{out.antitarget_file | quote}}  # pyright: ignore
-reffile = {{envs.ref | quote}}  # pyright: ignore
-cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
-method = {{envs.method | quote}}  # pyright: ignore
-bp_per_bin = {{envs.bp_per_bin | repr}}  # pyright: ignore
-target_max_size = {{envs.target_max_size | repr}}  # pyright: ignore
-target_min_size = {{envs.target_min_size | repr}}  # pyright: ignore
-antitarget_max_size = {{envs.antitarget_max_size | repr}}  # pyright: ignore
-antitarget_min_size = {{envs.antitarget_min_size | repr}}  # pyright: ignore
-annotate = {{envs.annotate | repr}}  # pyright: ignore
-short_names = {{envs.short_names | repr}}  # pyright: ignore
+bamfiles: list[Path] = {{in.bamfiles | each: as_path}}  # pyright: ignore # noqa
+accfile: str | None = {{in.accfile | quote}}  # pyright: ignore
+baitfile: str | None = {{in.baitfile | quote}}  # pyright: ignore
+target_file: str | None = {{out.target_file | quote}}  # pyright: ignore
+antitarget_file: str | None = {{out.antitarget_file | quote}}  # pyright: ignore
+reffile: str = {{envs.ref | quote}}  # pyright: ignore
+cnvkit: str = {{envs.cnvkit | quote}}  # pyright: ignore
+method: str = {{envs.method | quote}}  # pyright: ignore
+bp_per_bin: int = {{envs.bp_per_bin | repr}}  # pyright: ignore
+target_max_size: int = {{envs.target_max_size | repr}}  # pyright: ignore
+target_min_size: int = {{envs.target_min_size | repr}}  # pyright: ignore
+antitarget_max_size: int = {{envs.antitarget_max_size | repr}}  # pyright: ignore
+antitarget_min_size: int = {{envs.antitarget_min_size | repr}}  # pyright: ignore
+annotate: str | None = {{envs.annotate | quote}}  # pyright: ignore
+short_names: bool = {{envs.short_names | repr}}  # pyright: ignore
+
+if baitfile == "None":
+    baitfile = None
+if accfile == "None":
+    accfile = None
 
 
 def main():
 
-    args = dict(
-        f=reffile,
+    args: dict = dict(
+        f=Path(reffile).expanduser(),
         m=method,
         g=accfile,
         t=baitfile,
@@ -29,7 +37,7 @@ def main():
         target_min_size=target_min_size,
         antitarget_max_size=antitarget_max_size,
         antitarget_min_size=antitarget_min_size,
-        annotate=annotate,
+        annotate=False if annotate is None else Path(annotate).expanduser(),
         short_names=short_names,
         target_output_bed=target_file,
         antitarget_output_bed=antitarget_file,

biopipen/scripts/cnvkit/CNVkitBatch.py

@@ -3,8 +3,8 @@ from pathlib import Path
 import pandas
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-metafile = {{in.cnsfile | quote}}  # pyright: ignore
-outdir = {{out.outdir | quote}}  # pyright: ignore
+metafile: str = {{in.cnsfile | quote}}  # pyright: ignore  # noqa
+outdir: str = {{out.outdir | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 method = {{envs.method | quote}}  # pyright: ignore
 segment_method = {{envs.segment_method | quote}}  # pyright: ignore
@@ -13,7 +13,7 @@ count_reads = {{envs.count_reads | repr}}  # pyright: ignore
 drop_low_coverage = {{envs.drop_low_coverage | repr}}  # pyright: ignore
 ncores = {{envs.ncores | repr}}  # pyright: ignore
 rscript = {{envs.rscript | quote}}  # pyright: ignore
-ref = {{envs.ref | quote}}  # pyright: ignore
+ref: str = {{envs.ref | quote}}  # pyright: ignore
 targets = {{envs.targets | repr}}  # pyright: ignore
 antitargets = {{envs.antitargets | repr}}  # pyright: ignore
 annotate = {{envs.annotate | repr}}  # pyright: ignore
@@ -30,7 +30,7 @@ scatter = {{envs.scatter | repr}}  # pyright: ignore
 diagram = {{envs.diagram | repr}}  # pyright: ignore
 type_tumor = {{envs.type_tumor | repr}}  # pyright: ignore
 type_normal = {{envs.type_normal | repr}}  # pyright: ignore
-type_col = {{envs.type_col | quote}}  # pyright: ignore
+type_col: str = {{envs.type_col | quote}}  # pyright: ignore
 
 
 def gen_access():
@@ -38,11 +38,11 @@ def gen_access():
         return access
 
     accessfile = Path(outdir) / "access.bed"
-    args = dict(
+    args: dict = dict(
         exclude=access_excludes or False,
         s=access_min_gap_size or False,
         o=accessfile,
-        _=ref,
+        _=Path(ref).expanduser(),
     )
     args[""] = [cnvkit, "access"]
     run_command(dict_to_cli_args(args, dashify=True), fg=True)

biopipen/scripts/cnvkit/CNVkitCall.py

@@ -1,14 +1,14 @@
 from pathlib import Path
 from biopipen.utils.misc import run_command
 
-cnsfile = {{in.cnsfile | quote}}  # pyright: ignore
-cnrfile = {{in.cnrfile | quote}}  # pyright: ignore
+cnsfile: str = {{in.cnsfile | quote}}  # pyright: ignore  # noqa
+cnrfile: str = {{in.cnrfile | quote}}  # pyright: ignore
 vcf = {{in.vcf | repr}}  # pyright: ignore
 sample_id = {{in.sample_id | repr}}  # pyright: ignore
 normal_id = {{in.normal_id | repr}}  # pyright: ignore
 sample_sex = {{in.sample_sex | repr}}  # pyright: ignore
 purity = {{in.purity | repr}}  # pyright: ignore
-outdir = {{out.outdir | quote}}  # pyright: ignore
+outdir: str = {{out.outdir | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 center = {{envs.center | repr}}  # pyright: ignore
 center_at = {{envs.center_at | repr}}  # pyright: ignore

biopipen/scripts/cnvkit/CNVkitCoverage.py

@@ -1,9 +1,10 @@
+from pathlib import Path
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-bamfile = {{in.bamfile | quote}}  # pyright: ignore
+bamfile: str = {{in.bamfile | quote}}  # pyright: ignore  # noqa
 target_file = {{in.target_file | quote}}  # pyright: ignore
 outfile = {{out.outfile | quote}}  # pyright: ignore
-reffile = {{envs.reffile | quote}}  # pyright: ignore
+reffile: str = {{envs.reffile | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 count = {{envs.count | repr}}  # pyright: ignore
 min_mapq = {{envs.min_mapq | repr}}  # pyright: ignore
@@ -13,7 +14,7 @@ ncores = {{envs.ncores | repr}}  # pyright: ignore
 def main():
 
     args = dict(
-        f=reffile,
+        f=Path(reffile).expanduser(),
         c=count,
         q=min_mapq,
         p=ncores,

biopipen/scripts/cnvkit/CNVkitDiagram.py

@@ -4,10 +4,10 @@ from diot import Diot
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
 
-cnrfile = {{in.cnrfile | quote}}  # pyright: ignore
+cnrfile = {{in.cnrfile | quote}}  # pyright: ignore  # noqa
 cnsfile = {{in.cnsfile | quote}}  # pyright: ignore
 sample_sex = {{in.sample_sex | repr}}  # pyright: ignore
-outdir = {{out.outdir | quote}}  # pyright: ignore
+outdir: str = {{out.outdir | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 convert = {{envs.convert | quote}}  # pyright: ignore
 convert_args = {{envs.convert_args | repr}}  # pyright: ignore
@@ -16,7 +16,7 @@ min_probes = {{envs.min_probes | repr}}  # pyright: ignore
 male_reference = {{envs.male_reference | repr}}  # pyright: ignore
 no_shift_xy = {{envs.no_shift_xy | repr}}  # pyright: ignore
 title = {{envs.title | repr}}  # pyright: ignore
-cases = {{envs.cases | repr}}  # pyright: ignore
+cases: dict | None = {{envs.cases | repr}}  # pyright: ignore
 
 
 def do_case(name, case):
@@ -35,7 +35,7 @@ def do_case(name, case):
     pdffile = Path(outdir).joinpath(f"{name}.heatmap.pdf")
     pngfile = Path(outdir).joinpath(f"{name}.heatmap.png")
 
-    args = dict(
+    args: dict = dict(
         **case,
         s=cnsfile,
         o=pdffile,
@@ -44,7 +44,7 @@ def do_case(name, case):
     args[""] = [cnvkit, "diagram"]
     run_command(dict_to_cli_args(args, dashify=True), fg=True)
 
-    conv_args = dict(**conv_args, _=[pdffile, pngfile])
+    conv_args: dict = dict(**conv_args, _=[pdffile, pngfile])
     conv_args[""] = [convert]
     run_command(
         dict_to_cli_args(conv_args, prefix="-", dashify=True),

biopipen/scripts/cnvkit/CNVkitFix.py

@@ -2,11 +2,11 @@ from pathlib import Path
 
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-target_file = {{in.target_file | quote}}  # pyright: ignore
+target_file = {{in.target_file | quote}}  # pyright: ignore  # noqa
 antitarget_file = {{in.antitarget_file | quote}}  # pyright: ignore
 reference_file = {{in.reference | quote}}  # pyright: ignore
 sample_id = {{in.sample_id | repr}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
+outfile: str = {{out.outfile | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 cluster = {{envs.cluster | repr}}  # pyright: ignore
 no_gc = {{envs.no_gc | repr}}  # pyright: ignore
@@ -18,7 +18,7 @@ emptyfile.touch()
 
 def main():
 
-    args = dict(
+    args: dict = dict(
         i=sample_id,
         o=outfile,
         c=cluster,

biopipen/scripts/cnvkit/CNVkitGuessBaits.py

@@ -5,16 +5,16 @@ from pathlib import Path, PosixPath  # for as_path
 
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-bamfiles = {{in.bamfiles | repr}}  # pyright: ignore
-atfile = {{in.atfile | repr}}  # pyright: ignore
+bamfiles = {{in.bamfiles | each: str | repr}}  # pyright: ignore  # noqa
+atfile = {{in.atfile | quote}}  # pyright: ignore
 
-targetfile = {{out.targetfile | repr}}  # pyright: ignore
+targetfile = {{out.targetfile | quote}}  # pyright: ignore
 covfile = {{out.targetfile | as_path | attr: "with_suffix" | call: ".cnn" | repr}}  # pyright: ignore
 
-cnvkit = {{envs.cnvkit | repr}}  # pyright: ignore
+cnvkit: str = {{envs.cnvkit | repr}}  # pyright: ignore
 samtools = {{envs.samtools | repr}}  # pyright: ignore
 ncores = {{envs.ncores | repr}}  # pyright: ignore
-ref = {{envs.ref | repr}}  # pyright: ignore
+ref: str = {{envs.ref | repr}}  # pyright: ignore
 guided = {{envs.guided | repr}}  # pyright: ignore
 min_depth = {{envs.min_depth | repr}}  # pyright: ignore
 min_gap = {{envs.min_gap | repr}}  # pyright: ignore
@@ -32,10 +32,14 @@ else:
     params["min-gap"] = min_gap
     params["min-length"] = min_length
 
-biopipen_dir = {{biopipen_dir | repr}}  # pyright: ignore
+biopipen_dir: str = {{biopipen_dir | quote}}  # pyright: ignore
 
 # get the python path from cnvkit.py
-cnvkit_path = Path(which(cnvkit))
+cnvkit_found = which(cnvkit)
+if cnvkit_found is None:
+    raise ValueError(f"cnvkit executable not found: {cnvkit}")
+
+cnvkit_path = Path(cnvkit_found)
 # Modify cnvkit.py to a unique tmp path, named with timestamp
 # to find the python path
 tmp_cnvkit_path = Path("/tmp/cnvkit-{}.py".format(time.time()))
@@ -60,7 +64,7 @@ params.update({
     "o": targetfile,
     "c": covfile,
     "p": ncores,
-    "f": ref,
+    "f": Path(ref).expanduser(),
     "s": samtools,
     "_": bamfiles,
 })

biopipen/scripts/cnvkit/CNVkitHeatmap.py

@@ -1,12 +1,12 @@
 from pathlib import Path
 
-from diot import Diot
+from diot import Diot  # type: ignore[import]
 
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-segfiles = {{in.segfiles | repr}}  # pyright: ignore
+segfiles = {{in.segfiles | default: [] | each: str | repr}}  # pyright: ignore # noqa  # noqa
 sample_sex = {{in.sample_sex | repr}}  # pyright: ignore
-outdir = {{out.outdir | repr}}  # pyright: ignore
+outdir: str = {{out.outdir | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 convert = {{envs.convert | quote}}  # pyright: ignore
 convert_args = {{envs.convert_args | repr}}  # pyright: ignore
@@ -16,7 +16,7 @@ desaturate= {{ envs.desaturate | repr}}  # pyright: ignore
 male_reference= {{ envs.male_reference | repr}}  # pyright: ignore
 no_shift_xy= {{ envs.no_shift_xy | repr}}  # pyright: ignore
 order = {{envs.order | repr}}  # pyright: ignore
-cases = {{envs.cases | repr}}  # pyright: ignore
+cases: dict | None = {{envs.cases | repr}}  # pyright: ignore
 
 
 def parse_order(files, orderfile):
@@ -70,7 +70,7 @@ def do_case(name, case):
     args[""] = [cnvkit, "heatmap"]
     run_command(dict_to_cli_args(args, dashify=True), fg=True)
 
-    conv_args = dict(**conv_args, _=[pdffile, pngfile])
+    conv_args: dict = dict(**conv_args, _=[pdffile, pngfile])
     conv_args[""] = [convert]
     run_command(
         dict_to_cli_args(conv_args, dashify=True, prefix="-"),

biopipen/scripts/cnvkit/CNVkitReference.py

@@ -1,11 +1,12 @@
+from pathlib import Path
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-covfiles = {{in.covfiles | repr}}  # pyright: ignore
-target_file = {{in.target_file | repr}}  # pyright: ignore
-antitarget_file = {{in.antitarget_file | repr}}  # pyright: ignore
+covfiles = {{in.covfiles | default: [] | each: str | repr}}  # pyright: ignore  # noqa
+target_file = {{in.target_file | quote: quote_none=False}}  # pyright: ignore
+antitarget_file = {{in.antitarget_file | quote: quote_none=False}}  # pyright: ignore
 sample_sex = {{in.sample_sex | repr}}  # pyright: ignore
 outfile = {{out.outfile | quote}}  # pyright: ignore
-reffile = {{envs.ref | repr}}  # pyright: ignore
+reffile: str = {{envs.ref | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 cluster = {{envs.cluster | repr}}  # pyright: ignore
 min_cluster_size = {{envs.min_cluster_size | repr}}  # pyright: ignore
@@ -18,7 +19,7 @@ no_rmask = {{envs.no_rmask | repr}}  # pyright: ignore
 def main():
 
     args = dict(
-        f=reffile,
+        f=Path(reffile).expanduser(),
         o=outfile,
         c=cluster,
         min_cluster_size=min_cluster_size,

biopipen/scripts/cnvkit/CNVkitScatter.py

@@ -4,14 +4,14 @@ from diot import Diot
 
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-cnrfile = {{in.cnrfile | quote}}  # pyright: ignore
+cnrfile = {{in.cnrfile | quote}}  # pyright: ignore  # noqa
 cnsfile = {{in.cnsfile | quote}}  # pyright: ignore
 convert = {{envs.convert | quote}}  # pyright: ignore
 convert_args = {{envs.convert_args | repr}}  # pyright: ignore
 vcf = {{in.vcf | repr}}  # pyright: ignore
 sample_id = {{in.sample_id | repr}}  # pyright: ignore
 normal_id = {{in.normal_id | repr}}  # pyright: ignore
-outdir = {{out.outdir | quote}}  # pyright: ignore
+outdir: str = {{out.outdir | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 chromosome = {{envs.chromosome | repr}}  # pyright: ignore
 gene = {{envs.gene | repr}}  # pyright: ignore
@@ -25,7 +25,7 @@ y_min = {{envs.y_min | repr}}  # pyright: ignore
 min_variant_depth = {{envs.min_variant_depth | repr}}  # pyright: ignore
 zygosity_freq = {{envs.zygosity_freq | repr}}  # pyright: ignore
 title = {{envs.title | repr}}  # pyright: ignore
-cases = {{envs.cases | repr}}  # pyright: ignore
+cases: dict | None = {{envs.cases | repr}}  # pyright: ignore
 
 
 def do_case(name, case):
@@ -50,7 +50,7 @@ def do_case(name, case):
     pdffile = Path(outdir).joinpath(f"{name}.heatmap.pdf")
     pngfile = Path(outdir).joinpath(f"{name}.heatmap.png")
 
-    args = dict(
+    args: dict = dict(
         **case,
         s=cnsfile,
         o=pdffile,
@@ -62,7 +62,7 @@ def do_case(name, case):
     args[""] = [cnvkit, "scatter"]
     run_command(dict_to_cli_args(args, dashify=True), fg=True)
 
-    conv_args = dict(**conv_args, _=[pdffile, pngfile])
+    conv_args: dict = dict(**conv_args, _=[pdffile, pngfile])
     conv_args[""] = [convert]
     run_command(
         dict_to_cli_args(conv_args, dashify=True, prefix="-"),

biopipen/scripts/cnvkit/CNVkitSegment.py

@@ -2,11 +2,11 @@ from pathlib import Path
 
 from biopipen.utils.misc import run_command, dict_to_cli_args
 
-cnrfile = {{in.cnrfile | quote}}  # pyright: ignore
+cnrfile = {{in.cnrfile | quote}}  # pyright: ignore  # noqa
 vcf = {{in.vcf | repr}}  # pyright: ignore
 sample_id = {{in.sample_id | repr}}  # pyright: ignore
 normal_id = {{in.normal_id | repr}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
+outfile: str = {{out.outfile | quote}}  # pyright: ignore
 cnvkit = {{envs.cnvkit | quote}}  # pyright: ignore
 method = {{envs.method | quote}}  # pyright: ignore
 threshold = {{envs.threshold | repr}}  # pyright: ignore
@@ -21,7 +21,7 @@ zygosity_freq = {{envs.zygosity_freq | repr}}  # pyright: ignore
 
 def main():
 
-    args = dict(
+    args: dict = dict(
         o=outfile,
         d=Path(outfile).parent / "intermediate.rds",
         m=method,
@@ -39,8 +39,8 @@ def main():
         _=cnrfile,
     )
     args[""] = [cnvkit, "segment"]
-    args = dict_to_cli_args(args, dashify=True)
-    run_command(args, fg=True)
+    cmd_args = dict_to_cli_args(args, dashify=True)
+    run_command(cmd_args, fg=True)
 
 
 if __name__ == "__main__":