biopipen 0.34.6__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/ns/scrna_metabolic_landscape.py

@@ -29,6 +29,10 @@ class MetabolicPathwayActivity(Proc):
 
     ![MetabolicPathwayActivity_violin](https://pwwang.github.io/immunopipe/latest/processes/images/MetabolicPathwayActivity_violin.png){: width="45%"}
 
+    You may also have a merged heatmap to show all subsets in one plot.
+
+    ![MetabolicPathwayActivity_merged_heatmap](https://pwwang.github.io/immunopipe/latest/processes/images/MetabolicPathwayActivity_merged_heatmap.png){: width="80%"}
+
     Input:
         sobjfile: The Seurat object file.
             It should be loaded as a Seurat object

biopipen/ns/tcr.py

@@ -1163,10 +1163,10 @@ class Attach2Seurat(Proc):
     script = "file://../scripts/tcr/Attach2Seurat.R"
 
 
-class TCRClustering(Proc):
-    """Cluster the TCR clones by their CDR3 sequences
+class CDR3Clustering(Proc):
+    """Cluster the TCR/BCR clones by their CDR3 sequences
 
-    This process is used to cluster TCR clones based on their CDR3 sequences.
+    This process is used to cluster TCR/BCR clones based on their CDR3 sequences.
 
     It uses either
 
@@ -1190,7 +1190,7 @@ class TCRClustering(Proc):
     yield similar results.
 
     A text file will be generated with the cluster assignments for each cell, together
-    with the `immunarch` object (in `R`) with the cluster assignments at `TCR_Clsuter`
+    with the `immunarch` object (in `R`) with the cluster assignments at `CDR3_Clsuter`
     column. This information will then be merged to a `Seurat` object for further
     downstream analysis.
 
@@ -1200,14 +1200,20 @@ class TCRClustering(Proc):
     CDR3 sequence may be shared by multiple cells.
 
     Input:
-        screpfile: The TCR data object loaded by `scRepertoire::CombineTCR()` or
-            `scRepertoire::CombineExpression()`
+        screpfile: The TCR/BCR data object loaded by `scRepertoire::CombineTCR()`,
+            `scRepertoire::CombineBCR()` or `scRepertoire::CombineExpression()`
 
     Output:
-        outfile: The `scRepertoire` object in qs with TCR cluster information.
-            Column `TCR_Cluster` will be added to the metadata.
+        outfile: The `scRepertoire` object in qs with TCR/BCR cluster information.
+            Column `CDR3_Cluster` will be added to the metadata.
 
     Envs:
+        type (choice): The type of the data.
+            - TCR: T cell receptor data
+            - BCR: B cell receptor data
+            - auto: Automatically detect the type from the data.
+                Try to find TRB or IGH genes in the CTgene column to determine
+                whether it is TCR or BCR data.
         tool (choice): The tool used to do the clustering, either
             [GIANA](https://github.com/s175573/GIANA) or
             [ClusTCR](https://github.com/svalkiers/clusTCR).
@@ -1216,7 +1222,7 @@ class TCRClustering(Proc):
             - ClusTCR: by Sebastiaan Valkiers, etc
         python: The path of python with `GIANA`'s dependencies installed
             or with `clusTCR` installed. Depending on the `tool` you choose.
-        within_sample (flag): Whether to cluster the TCR clones within each sample.
+        within_sample (flag): Whether to cluster the TCR/BCR clones within each sample.
             When `in.screpfile` is a `Seurat` object, the samples are marked by
             the `Sample` column in the metadata.
         args (type=json): The arguments for the clustering tool
@@ -1224,10 +1230,22 @@ class TCRClustering(Proc):
             See <https://github.com/s175573/GIANA#usage>.
             For ClusTCR, they will be passed to `clustcr.Clustering(...)`
             See <https://svalkiers.github.io/clusTCR/docs/clustering/how-to-use.html#clustering>.
-        chain (choice): The TCR chain to use for clustering.
-            - alpha: TCR alpha chain (the first sequence in CTaa, separated by `_`)
-            - beta: TCR beta chain (the second sequence in CTaa, separated by `_`)
-            - both: Both TCR alpha and beta chains
+        chain (choice): The TCR/BCR chain to use for clustering.
+            - heavy: The heavy chain, TRB for TCR, IGH for BCR.
+                For TCR, TRB is the second sequence in `CTaa`, separated by `_` if
+                input is a Seurat object; otherwise, it is extracted from the `cdr3_aa2` column.
+                For BCR, IGH is the first sequence in `CTaa`, separated by `_` if
+                input is a Seurat object; otherwise, it is extracted from the `cdr3_aa1` column.
+            - light: The light chain, TRA for TCR, IGL/IGK for BCR.
+                For TCR, TRA is the first sequence in `CTaa`, separated by `_` if
+                input is a Seurat object; otherwise, it is extracted from the `cdr3_aa1` column.
+                For BCR, IGL/IGK is the second sequence in `CTaa`, separated by `_` if
+                input is a Seurat object; otherwise, it is extracted from the `cdr3_aa2` column.
+            - TRA: Only the TRA chain for TCR (light chain).
+            - TRB: Only the TRB chain for TCR (heavy chain).
+            - IGH: Only the IGH chain for BCR (heavy chain).
+            - IGLK: Only the IGL/IGK chain for BCR (light chain).
+            - both: Both sequences from the heavy and light chains (CTaa column).
 
     Requires:
         clusTCR:
@@ -1238,13 +1256,14 @@ class TCRClustering(Proc):
     output = "outfile:file:{{in.screpfile | stem}}.tcr_clustered.qs"
     lang = config.lang.rscript
     envs = {
+        "type": "auto",  # or TCR, BCR
         "tool": "GIANA",  # or ClusTCR
         "python": config.lang.python,
         "within_sample": True,  # whether to cluster the TCR clones within each sample
         "args": {},
-        "chain": "both",  # alpha, beta, both
+        "chain": "both",
     }
-    script = "file://../scripts/tcr/TCRClustering.R"
+    script = "file://../scripts/tcr/CDR3Clustering.R"
 
 
 @mark(deprecated="{proc.name} is deprecated, use ClonalStats instead.")
@@ -1805,6 +1824,225 @@ class ClonalStats(Proc):
     Using [`scplotter`](https://github.com/pwwang/scplotter) to visualize the clonal
     information.
 
+    Examples:
+        ### Clonal Volume
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Volume"]
+        viz_type = "volume"
+        x_text_angle = 45
+        ```
+
+        ![Clonal_Volume](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Number-of-Clones/Clonal-Volume.png){: width="80%"}
+
+        ### Clonal Volume by Diagnosis
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Volume by Diagnosis"]
+        viz_type = "volume"
+        x = "seurat_clusters"
+        group_by = "Diagnosis"
+        comparisons = true
+        ```
+
+        ![Clonal_Volume_by_Diagnosis](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Number-of-Clones/Clonal-Volume-by-Diagnosis.png){: width="80%"}
+
+        ### Clonal Abundance
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Abundance"]
+        viz_type = "abundance"
+        ```
+
+        ![Clonal_Abundance](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Abundance/Clonal-Abundance.png){: width="80%"}
+
+        ### Clonal Abundance Density
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Abundance Density"]
+        viz_type = "abundance"
+        plot_type = "density"
+        ```
+
+        ![Clonal_Abundance_Density](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Abundance/Clonal-Abundance-Density.png){: width="80%"}
+
+        ### CDR3 Length
+
+        ```toml
+        [ClonalStats.envs.cases."CDR3 Length"]
+        viz_type = "length"
+        ```
+
+        ![CDR3_Length](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Sequence-Length/CDR3-Length.png){: width="80%"}
+
+        ### CDR3 Length (Beta Chain)
+
+        ```toml
+        [ClonalStats.envs.cases."CDR3 Length (Beta Chain)"]
+        viz_type = "length"
+        chain = "TRB"
+        ```
+
+        ![CDR3_Length_Beta_Chain](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Sequence-Length/CDR3-Length-Beta-Chain-.png){: width="80%"}
+
+        ### Clonal Residency
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Residency"]
+        viz_type = "residency"
+        group_by = "Diagnosis"
+        chain = "TRB"
+        clone_call = "gene"
+        groups = ["Colitis", "NoColitis"]
+        ```
+
+        ![Clonal_Residency](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Residency/Clonal-Residency.png){: width="80%"}
+
+        ### Clonal Residency (UpSet Plot)
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Residency (UpSet Plot)"]
+        viz_type = "residency"
+        plot_type = "upset"
+        group_by = "Diagnosis"
+        chain = "TRB"
+        clone_call = "gene"
+        groups = ["Colitis", "NoColitis"]
+        devpars = {width = 800}
+        ```
+
+        ![Clonal_Residency_UpSet_Plot](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Residency/Clonal-Residency-UpSet-Plot-.png){: width="80%"}
+
+        ### Clonal Statistics with Expanded Clones
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Statistics with Expanded Clones"]
+        viz_type = "stat"
+        plot_type = "pies"
+        group_by = "Diagnosis"
+        groups = ["Colitis", "NoColitis"]
+        clones = {"Expanded Clones In Colitis" = "sel(Colitis > 2)", "Expanded Clones In NoColitis" = "sel(NoColitis > 2)"}
+        subgroup_by = "seurat_clusters"
+        pie_size = "sqrt"
+        show_row_names = true
+        show_column_names = true
+        devpars = {width = 720}
+        ```
+
+        ![Clonal_Statistics_with_Expanded_Clones](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Statistics/Clonal-Statistics-with-Expanded-Clones.png){: width="80%"}
+
+        ### Hyperexpanded Clonal Dynamics
+
+        ```toml
+        [ClonalStats.envs.cases."Hyperexpanded Clonal Dynamics"]
+        viz_type = "stat"
+        plot_type = "sankey"
+        group_by = "Diagnosis"
+        chain = "TRB"
+        groups = ["Colitis", "NoColitis"]
+        clones = {"Hyper-Expanded Clones In Colitis" = "sel(Colitis > 5)", "Hyper-Expanded Clones In NoColitis" = "sel(NoColitis > 5)"}
+        devpars = {width = 800}
+        ```
+
+        ![Hyperexpanded_Clonal_Dynamics](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Statistics/Hyperexpanded-Clonal-Dynamics.png){: width="80%"}
+
+        ### Clonal Composition
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Composition"]
+        viz_type = "composition"
+        x_text_angle = 45
+        ```
+
+        ![Clonal_Composition](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Composition.png){: width="80%"}
+
+        ### Clonal Overlapping
+
+        ```toml
+        viz_type = "overlap"
+        chain = "TRB"
+        clone_call = "gene"
+        ```
+
+        ![Clonal_Overlapping](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Overlapping.png){: width="80%"}
+
+        ### Clonal Diversity
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Diversity"]
+        # method = "shannon"  # default
+        viz_type = "diversity"
+        x_text_angle = 45
+        ```
+
+        ![Clonal_Diversity](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Diversity/Clonal-Diversity.png){: width="80%"}
+
+        ### Clonal Diversity (gini.coeff, by Diagnosis)
+
+        ```toml
+        [ClonalStats.envs.cases."Clonal Diversity (gini.coeff, by Diagnosis)"]
+        method = "gini.coeff"
+        viz_type = "diversity"
+        plot_type = "box"
+        group_by = "Diagnosis"
+        comparisons = true
+        devpars = {height = 600, width = 600}
+        ```
+
+        ![Clonal_Diversity_gini_coeff_by_Diagnosis](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Clonal-Diversity/Clonal-Diversity-gini-coeff-by-Diagnosis-.png){: width="80%"}
+
+        ### Gene Usage Frequency
+
+        ```toml
+        [ClonalStats.envs.cases."Gene Usage Frequency"]
+        viz_type = "geneusage"
+        devpars = {width = 1200}
+        ```
+
+        ![Gene_Usage_Frequency](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Gene-Usage-Frequency.png){: width="80%"}
+
+        ### Positional amino acid frequency
+
+        ```toml
+        [ClonalStats.envs.cases."Positional amino acid frequency"]
+        viz_type = "positional"
+        # method = "AA"  # default
+        devpars = {width = 1600}
+        ```
+
+        ![Positional_amino_acid_frequency](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Positional-Properties/Positional-amino-acid-frequency.png){: width="80%"}
+
+        ### Positional shannon entropy
+
+        ```toml
+        [ClonalStats.envs.cases."Positional shannon entropy"]
+        viz_type = "positional"
+        method = "shannon"
+        devpars = {width = 1200}
+        ```
+
+        ![Positional_shannon_entropy](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Positional-Properties/Positional-shannon-entropy.png){: width="80%"}
+
+        ### 3-Mer Frequency
+
+        ```toml
+        [ClonalStats.envs.cases."3-Mer Frequency"]
+        viz_type = "kmer"
+        k = 3  # default is 3
+        devpars = {width = 800}
+        ```
+
+        ![3_Mer_Frequency](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/3-Mer-Frequency.png){: width="80%"}
+
+        ### Rarefaction Curve
+
+        ```toml
+        [ClonalStats.envs.cases."Rarefaction Curve"]
+        viz_type = "rarefaction"
+        ```
+
+        ![Rarefaction_Curve](https://raw.githubusercontent.com/pwwang/immunopipe/tests-output/clonalstats/ClonalStats/sampleinfo.scRep.clonalstats/Rarefaction-Curve.png){: width="80%"}
+
     Input:
         screpfile: The `scRepertoire` object in RDS/qs format
 
@@ -1822,7 +2060,7 @@ class ClonalStats(Proc):
             - abundance: The abundance of the clones using [`ClonalAbundancePlot`](https://pwwang.github.io/scplotter/reference/ClonalAbundancePlot.html)
             - length: The length of the CDR3 sequences using [`ClonalLengthPlot`](https://pwwang.github.io/scplotter/reference/ClonalLengthPlot.html)
             - residency: The residency of the clones using [`ClonalResidencyPlot`](https://pwwang.github.io/scplotter/reference/ClonalResidencyPlot.html)
-            - dynamics: The dynamics of the clones using [`ClonalDynamicsPlot`](https://pwwang.github.io/scplotter/reference/ClonalDynamicsPlot.html)
+            - stats: The stats of the clones using [`ClonalStatsPlot`](https://pwwang.github.io/scplotter/reference/ClonalStatsPlot.html)
             - composition: The composition of the clones using [`ClonalCompositionPlot`](https://pwwang.github.io/scplotter/reference/ClonalCompositionPlot.html)
             - overlap: The overlap of the clones using [`ClonalOverlapPlot`](https://pwwang.github.io/scplotter/reference/ClonalOverlapPlot.html)
             - diversity: The diversity of the clones using [`ClonalDiversityPlot`](https://pwwang.github.io/scplotter/reference/ClonalDiversityPlot.html)
@@ -1842,6 +2080,7 @@ class ClonalStats(Proc):
         save_code (flag): Whether to save the code used to generate the plots
             Note that the data directly used to generate the plots will also be saved in an `rda` file.
             Be careful if the data is large as it may take a lot of disk space.
+        save_data (flag): Whether to save the data used to generate the plot.
         descr: The description of the plot, used to show in the report.
         <more>: The arguments for the plot function
             See the documentation of the corresponding plot function for the details
@@ -1865,6 +2104,7 @@ class ClonalStats(Proc):
         "devpars": {"width": None, "height": None, "res": 100},
         "more_formats": [],
         "save_code": False,
+        "save_data": False,
         "descr": None,
         "cases": {
             "Clonal Volume": {"viz_type": "volume"},

biopipen/ns/web.py

@@ -31,8 +31,13 @@ class Download(Proc):
     """
     input = "url"
     output = (
+        # Need to replace http:// and https:// to avoid cloudpathlib.AnyPath to get
+        # the basename for something like "https://example.com/data/?file=datafile.txt"
+        # as data, but "?file=datafile.txt"
         "outfile:file:"
         """{{in.url
+            | replace: 'http://', ''
+            | replace: 'https://', ''
             | basename
             | url_decode
             | slugify: separator='.', lowercase=False, regex_pattern='[^-a-zA-Z0-9_]+'

biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte

@@ -50,6 +50,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 </ListItem>
 </UnorderedList>
 
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
 {%- macro report_job(job, h=1) -%}
     {{ job | render_job: h=h }}
 {%- endmacro -%}
@@ -59,12 +68,3 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
-
-<style>
-.listitem {
-    font-size: large;
-    font-weight: bold;
-    margin: 1rem 0 0.5rem 0;
-    display: inline-block;
-}
-</style>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -82,6 +82,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 </ListItem>
 </UnorderedList>
 
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
 {%- macro report_job(job, h=1) -%}
     {{ job | render_job: h=h }}
 {%- endmacro -%}
@@ -92,11 +101,3 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 
 {{ report_jobs(jobs, head_job, report_job) }}
 
-<style>
-.listitem {
-    font-size: large;
-    font-weight: bold;
-    margin: 1rem 0 0.5rem 0;
-    display: inline-block;
-}
-</style>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte

@@ -61,6 +61,15 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 </ListItem>
 </UnorderedList>
 
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
 {%- macro report_job(job, h=1) -%}
     {{ job | render_job: h=h }}
 {%- endmacro -%}
@@ -70,12 +79,3 @@ The cells are grouped at 2 dimensions: `subset_by`, usually the clinic groups th
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
-
-<style>
-.listitem {
-    font-size: large;
-    font-weight: bold;
-    margin: 1rem 0 0.5rem 0;
-    display: inline-block;
-}
-</style>

biopipen/reports/tcr/ClonalStats.svelte

@@ -2,6 +2,7 @@
 
 <script>
     import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, UnorderedList, ListItem, InlineNotification } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}

biopipen/scripts/cellranger/CellRangerCount.py

@@ -1,12 +1,13 @@
-import uuid
+from contextlib import suppress
+import hashlib
+import shutil
 import re
-import os.path
 from pathlib import Path, PosixPath  # noqa: F401
 from biopipen.utils.misc import run_command
 
 fastqs: list[Path] = {{in.fastqs | each: as_path}}  # pyright: ignore  # noqa
-outdir: str = {{out.outdir | quote}}  # pyright: ignore
-id = {{out.outdir | basename | quote}}  # pyright: ignore
+outdir: Path = Path({{out.outdir | quote}})  # pyright: ignore
+id: str = {{out.outdir | basename | quote}}  # pyright: ignore
 
 cellranger = {{envs.cellranger | quote}}  # pyright: ignore
 tmpdir = Path({{envs.tmpdir | quote}})  # pyright: ignore
@@ -14,12 +15,18 @@ ref: str = {{envs.ref | quote}}  # pyright: ignore
 ncores = {{envs.ncores | int}}  # pyright: ignore
 include_introns = {{envs.include_introns | repr}}  # pyright: ignore
 create_bam = {{envs.create_bam | repr}}  # pyright: ignore
+outdir_is_mounted: bool = {{envs.outdir_is_mounted | repr}}  # pyright: ignore
+copy_outs_only: bool = {{envs.copy_outs_only | repr}}  # pyright: ignore
 
+ref: Path = Path(ref).resolve()  # pyright: ignore
+if not ref.exists():
+    raise FileNotFoundError(f"Reference path does not exist: {ref}")
 include_introns = str(include_introns).lower()
 create_bam = str(create_bam).lower()
 
 # create a temporary unique directory to store the soft-linked fastq files
-fastqdir = tmpdir / f"cellranger_count_{uuid.uuid4()}"
+uid = hashlib.md5(str(fastqs).encode()).hexdigest()[:8]
+fastqdir = tmpdir / f"cellranger_count_{uid}"
 fastqdir.mkdir(parents=True, exist_ok=True)
 if len(fastqs) == 1 and fastqs[0].is_dir():
     fastqs = list(fastqs[0].glob("*.fastq.gz"))
@@ -39,7 +46,7 @@ for fastq in fastqs:
 
     linked.symlink_to(fastq)
 
-other_args = {{envs | dict_to_cli_args: dashify=True, exclude=['no_bam', 'create_bam', 'include_introns', 'cellranger', 'transcriptome', 'ref', 'tmpdir', 'id', 'ncores']}}  # pyright: ignore
+other_args = {{envs | dict_to_cli_args: dashify=True, exclude=['no_bam', 'create_bam', 'include_introns', 'cellranger', 'transcriptome', 'ref', 'tmpdir', 'id', 'ncores', 'outdir_is_mounted', 'copy_outs_only']}}  # pyright: ignore
 
 command = [
     cellranger,
@@ -49,7 +56,7 @@ command = [
     "--fastqs",
     fastqdir,
     "--transcriptome",
-    Path(ref).resolve(),
+    str(ref),
     "--localcores",
     ncores,
     "--disable-ui",
@@ -62,18 +69,29 @@ command = [
 #   cellranger cellranger-7.2.0
 version: str = run_command([cellranger, "--version"], stdout = "RETURN")  # type: ignore
 version = version.replace("cellranger", "").replace("-", "").strip()  # type: ignore
+print(f"# Detected cellranger version: {version}")
 version: list[int] = list(map(int, version.split(".")))  # type: ignore
 if version[0] >= 8:
     command += ["--create-bam", create_bam]
 elif create_bam != "true":
     command += ["--no-bam"]
 
-run_command(command, fg=True, cwd=str(Path(outdir).parent))
+if outdir_is_mounted:
+    print("# Using mounted outdir, redirecting cellranger output to a local tmpdir")
+    local_outdir = tmpdir / f"{outdir.name}-{uid}" / id
+    if local_outdir.parent.exists():
+        shutil.rmtree(local_outdir.parent)
+    local_outdir.parent.mkdir(parents=True, exist_ok=True)
+    odir = local_outdir
+else:
+    odir = outdir
 
-web_summary_html = Path(outdir) / "outs" / "web_summary.html"
+run_command(command, fg=True, cwd=str(odir.parent))
+
+web_summary_html = odir / "outs" / "web_summary.html"
 if not web_summary_html.exists():
     raise RuntimeError(
-        f"web_summary.html does not exist in {outdir}/outs. "
+        f"web_summary.html does not exist in {odir}/outs. "
         "cellranger count failed."
     )
 
@@ -81,7 +99,7 @@ if not web_summary_html.exists():
 # to void vscode live server breaking the page by injecting some code
 print("# Modify web_summary.html to move javascript to a separate file")
 try:
-    web_summary_js = Path(outdir) / "outs" / "web_summary.js"
+    web_summary_js = odir / "outs" / "web_summary.js"
     web_summary_content = web_summary_html.read_text()
     regex = re.compile(r"<script>(.+)</script>", re.DOTALL)
     web_summary_html.write_text(regex.sub(
@@ -92,3 +110,29 @@ try:
 except Exception as e:
     print(f"Error modifying web_summary.html: {e}")
     raise e
+
+# If using local tmpdir for output, move results to the final outdir
+if outdir_is_mounted:
+    print("# Copy results back to outdir")
+    if outdir.exists():
+        shutil.rmtree(outdir)
+
+    if copy_outs_only:
+        outdir.mkdir(parents=True, exist_ok=True)
+        with suppress(Exception):
+            # Some files may be failed to copy due to permission issues
+            # But the contents are actually copied
+            shutil.copytree(odir / "outs", outdir / "outs")
+    else:
+        with suppress(Exception):
+            shutil.copytree(local_outdir, outdir)  # type: ignore
+
+    # Make sure essential files exist
+    web_summary_html = outdir / "outs" / "web_summary.html"
+    web_summary_js = outdir / "outs" / "web_summary.js"
+    for f in [web_summary_html, web_summary_js]:
+        if not f.exists():
+            raise RuntimeError(
+                f"{f} does not exist in {outdir}/outs. "
+                "Copying results back from tmpdir failed."
+            )