From 3ba70b6e6cc1a2774a413c50bc2baa72214e4556 Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 18 Nov 2025 16:15:26 +0000 Subject: [PATCH] Build branch openpipeline_spatial/downgrade-squidpy with version downgrade-squidpy to openpipeline_spatial on branch downgrade-squidpy (6ac22db) Build pipeline: openpipelines-bio.openpipeline-spatial.downgrade-squidpy-ntjcd Source commit: https://github.com/openpipelines-bio/openpipeline_spatial/commit/6ac22db1075448735626eea2860ab5f3cd022348 Source message: update fov index --- src/base/requirements/anndata.yaml | 2 +- src/base/requirements/squidpy.yaml | 2 +- src/convert/from_cosmx_to_h5mu/script.py | 26 ++++++++++---- .../filter/subset_cosmx/.config.vsh.yaml | 4 +-- .../filter/subset_cosmx/subset_cosmx | 6 ++-- .../filter/subset_cosmx/.config.vsh.yaml | 4 +-- .../nextflow/filter/subset_cosmx/main.nf | 4 +-- .../from_cells2stats_to_h5mu/.config.vsh.yaml | 4 +-- .../from_cells2stats_to_h5mu | 6 ++-- .../from_cosmx_to_h5mu/.config.vsh.yaml | 8 ++--- .../from_cosmx_to_h5mu/from_cosmx_to_h5mu | 32 ++++++++++++----- .../.config.vsh.yaml | 2 +- .../from_cosmx_to_spatialexperiment | 4 +-- .../.config.vsh.yaml | 4 +-- .../from_h5mu_to_spatialexperiment | 4 +-- .../from_spatialdata_to_h5mu/.config.vsh.yaml | 4 +-- .../from_spatialdata_to_h5mu | 6 ++-- .../from_xenium_to_h5mu/.config.vsh.yaml | 4 +-- .../from_xenium_to_h5mu/from_xenium_to_h5mu | 6 ++-- .../.config.vsh.yaml | 2 +- .../from_xenium_to_spatialdata | 4 +-- .../.config.vsh.yaml | 2 +- .../from_xenium_to_spatialexperiment | 4 +-- .../spaceranger_count/.config.vsh.yaml | 2 +- .../spaceranger_count/spaceranger_count | 4 +-- .../from_cells2stats_to_h5mu/.config.vsh.yaml | 4 +-- .../convert/from_cells2stats_to_h5mu/main.nf | 4 +-- .../from_cosmx_to_h5mu/.config.vsh.yaml | 8 ++--- .../convert/from_cosmx_to_h5mu/main.nf | 34 +++++++++++++------ .../.config.vsh.yaml | 2 +- .../from_cosmx_to_spatialexperiment/main.nf | 2 +- .../.config.vsh.yaml | 4 +-- .../from_h5mu_to_spatialexperiment/main.nf | 4 +-- .../from_spatialdata_to_h5mu/.config.vsh.yaml | 4 +-- .../convert/from_spatialdata_to_h5mu/main.nf | 4 +-- .../from_xenium_to_h5mu/.config.vsh.yaml | 4 +-- .../convert/from_xenium_to_h5mu/main.nf | 4 +-- .../.config.vsh.yaml | 2 +- .../from_xenium_to_spatialdata/main.nf | 2 +- .../.config.vsh.yaml | 2 +- .../from_xenium_to_spatialexperiment/main.nf | 2 +- .../spaceranger_count/.config.vsh.yaml | 2 +- .../mapping/spaceranger_count/main.nf | 2 +- .../spatial_process_samples/.config.vsh.yaml | 2 +- .../spatial_process_samples/main.nf | 2 +- .../workflows/qc/spatial_qc/.config.vsh.yaml | 2 +- .../nextflow/workflows/qc/spatial_qc/main.nf | 2 +- 47 files changed, 145 insertions(+), 103 deletions(-) diff --git a/src/base/requirements/anndata.yaml b/src/base/requirements/anndata.yaml index 5f2a345..8ca4664 100644 --- a/src/base/requirements/anndata.yaml +++ b/src/base/requirements/anndata.yaml @@ -1,2 +1,2 @@ packages: - - anndata<0.11.0 + - anndata~=0.11.1 diff --git a/src/base/requirements/squidpy.yaml b/src/base/requirements/squidpy.yaml index c27a731..3d27832 100644 --- a/src/base/requirements/squidpy.yaml +++ b/src/base/requirements/squidpy.yaml @@ -1,3 +1,3 @@ __merge__: [/src/base/requirements/spatialdata.yaml, .] packages: - - squidpy<1.5.0 + - squidpy~=1.6.5 diff --git a/src/convert/from_cosmx_to_h5mu/script.py b/src/convert/from_cosmx_to_h5mu/script.py index 1f08796..9a14777 100644 --- a/src/convert/from_cosmx_to_h5mu/script.py +++ b/src/convert/from_cosmx_to_h5mu/script.py @@ -63,12 +63,26 @@ def main(): logger.info("Reading in CosMx data...") input_files = retrieve_input_data(par["input"]) - adata = sq.read.nanostring( - path=input_files["counts_file"].parent, - counts_file=input_files["counts_file"].name, - meta_file=input_files["meta_file"].name, - fov_file=input_files["fov_file"].name, - ) + try: + adata = sq.read.nanostring( + path=input_files["counts_file"].parent, + counts_file=input_files["counts_file"].name, + meta_file=input_files["meta_file"].name, + fov_file=input_files["fov_file"].name, + ) + except ValueError as e: + if "Index fov invalid" in str(e): + import pandas as pd + df = pd.read_csv(input_files["fov_file"]) + df.rename(columns={"FOV": "fov"}, inplace=True) + df.to_csv(input_files["fov_file"], index=False) + + adata = sq.read.nanostring( + path=input_files["counts_file"].parent, + counts_file=input_files["counts_file"].name, + meta_file=input_files["meta_file"].name, + fov_file=input_files["fov_file"].name, + ) logger.info("Writing output MuData object...") mdata = mu.MuData({par["modality"]: adata}) diff --git a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml index 40dd468..1222b62 100644 --- a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml +++ b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml @@ -203,7 +203,7 @@ engines: packages: - "spatialdata~=0.5.0" - "pyarrow~=18.0.0" - - "squidpy<1.5.0" + - "squidpy~=1.6.5" upgrade: true test_setup: - type: "apt" @@ -228,7 +228,7 @@ build_info: output: "target/_private/executable/filter/subset_cosmx" executable: "target/_private/executable/filter/subset_cosmx/subset_cosmx" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/_private/executable/filter/subset_cosmx/subset_cosmx b/target/_private/executable/filter/subset_cosmx/subset_cosmx index 96ce9ec..6619813 100755 --- a/target/_private/executable/filter/subset_cosmx/subset_cosmx +++ b/target/_private/executable/filter/subset_cosmx/subset_cosmx @@ -454,13 +454,13 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy<1.5.0" + pip install --upgrade --no-cache-dir "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy~=1.6.5" LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:47Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml index 9010f82..565f3ef 100644 --- a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml +++ b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml @@ -203,7 +203,7 @@ engines: packages: - "spatialdata~=0.5.0" - "pyarrow~=18.0.0" - - "squidpy<1.5.0" + - "squidpy~=1.6.5" upgrade: true test_setup: - type: "apt" @@ -228,7 +228,7 @@ build_info: output: "target/_private/nextflow/filter/subset_cosmx" executable: "target/_private/nextflow/filter/subset_cosmx/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/_private/nextflow/filter/subset_cosmx/main.nf b/target/_private/nextflow/filter/subset_cosmx/main.nf index cb603ce..813dc38 100644 --- a/target/_private/nextflow/filter/subset_cosmx/main.nf +++ b/target/_private/nextflow/filter/subset_cosmx/main.nf @@ -3297,7 +3297,7 @@ meta = [ "packages" : [ "spatialdata~=0.5.0", "pyarrow~=18.0.0", - "squidpy<1.5.0" + "squidpy~=1.6.5" ], "upgrade" : true } @@ -3334,7 +3334,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index efd345c..611776f 100644 --- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml @@ -271,7 +271,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "pyarrow" git: @@ -301,7 +301,7 @@ build_info: output: "target/executable/convert/from_cells2stats_to_h5mu" executable: "target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu index 8c5d308..f095936 100755 --- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu +++ b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu @@ -453,15 +453,15 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "pyarrow" && \ + pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "pyarrow" && \ pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \ python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")' LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml index 482f461..5861ec5 100644 --- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -199,11 +199,11 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "spatialdata~=0.5.0" - "pyarrow~=18.0.0" - - "squidpy<1.5.0" + - "squidpy~=1.6.5" - "pyarrow" git: - "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" @@ -230,7 +230,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" script: - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ @@ -247,7 +247,7 @@ build_info: output: "target/executable/convert/from_cosmx_to_h5mu" executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu index 076445b..0b69ebe 100755 --- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu +++ b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu @@ -454,15 +454,15 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy<1.5.0" "pyarrow" && \ + pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy~=1.6.5" "pyarrow" && \ pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \ python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")' LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER @@ -1199,12 +1199,26 @@ def main(): logger.info("Reading in CosMx data...") input_files = retrieve_input_data(par["input"]) - adata = sq.read.nanostring( - path=input_files["counts_file"].parent, - counts_file=input_files["counts_file"].name, - meta_file=input_files["meta_file"].name, - fov_file=input_files["fov_file"].name, - ) + try: + adata = sq.read.nanostring( + path=input_files["counts_file"].parent, + counts_file=input_files["counts_file"].name, + meta_file=input_files["meta_file"].name, + fov_file=input_files["fov_file"].name, + ) + except ValueError as e: + if "Index fov invalid" in str(e): + import pandas as pd + df = pd.read_csv(input_files["fov_file"]) + df.rename(columns={"FOV": "fov"}, inplace=True) + df.to_csv(input_files["fov_file"], index=False) + + adata = sq.read.nanostring( + path=input_files["counts_file"].parent, + counts_file=input_files["counts_file"].name, + meta_file=input_files["meta_file"].name, + fov_file=input_files["fov_file"].name, + ) logger.info("Writing output MuData object...") mdata = mu.MuData({par["modality"]: adata}) diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index fb85025..a27a2fa 100644 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -234,7 +234,7 @@ build_info: output: "target/executable/convert/from_cosmx_to_spatialexperiment" executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment index 23f9cbb..14b3333 100755 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment @@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml index cd79d16..5ca2e59 100644 --- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml @@ -207,7 +207,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" script: - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ @@ -224,7 +224,7 @@ build_info: output: "target/executable/convert/from_h5mu_to_spatialexperiment" executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment index 2315ff1..589c4f2 100755 --- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment +++ b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment @@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment" -LABEL org.opencontainers.image.created="2025-11-18T15:22:08Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:49Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index f131210..747bbd0 100644 --- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -190,7 +190,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "spatialdata~=0.5.0" - "pyarrow~=18.0.0" @@ -221,7 +221,7 @@ build_info: output: "target/executable/convert/from_spatialdata_to_h5mu" executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu index 0fc923e..32799dd 100755 --- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu +++ b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu @@ -454,14 +454,14 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" && \ + pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" && \ python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")' LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml index fabeee2..8e47e63 100644 --- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml @@ -213,7 +213,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "scanpy~=1.10.4" - "pyarrow" @@ -244,7 +244,7 @@ build_info: output: "target/executable/convert/from_xenium_to_h5mu" executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu index bd422b5..14c045c 100755 --- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu +++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu @@ -453,15 +453,15 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "scanpy~=1.10.4" "pyarrow" && \ + pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "scanpy~=1.10.4" "pyarrow" && \ pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \ python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")' LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml index 372d727..4cac123 100644 --- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -326,7 +326,7 @@ build_info: output: "target/executable/convert/from_xenium_to_spatialdata" executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata index a3311b1..a31703f 100755 --- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata +++ b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata" -LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 09121c6..2c7d835 100644 --- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -224,7 +224,7 @@ build_info: output: "target/executable/convert/from_xenium_to_spatialexperiment" executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment index 770abd5..9d8a98a 100755 --- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment +++ b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment @@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment" -LABEL org.opencontainers.image.created="2025-11-18T15:22:08Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:49Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/executable/mapping/spaceranger_count/.config.vsh.yaml b/target/executable/mapping/spaceranger_count/.config.vsh.yaml index 3fefed2..9a12122 100644 --- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml @@ -426,7 +426,7 @@ build_info: output: "target/executable/mapping/spaceranger_count" executable: "target/executable/mapping/spaceranger_count/spaceranger_count" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/mapping/spaceranger_count/spaceranger_count b/target/executable/mapping/spaceranger_count/spaceranger_count index 800d52a..c0ad82d 100755 --- a/target/executable/mapping/spaceranger_count/spaceranger_count +++ b/target/executable/mapping/spaceranger_count/spaceranger_count @@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count" -LABEL org.opencontainers.image.created="2025-11-18T15:22:08Z" +LABEL org.opencontainers.image.created="2025-11-18T15:52:49Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763" +LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348" LABEL org.opencontainers.image.version="downgrade-squidpy" VIASHDOCKER diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index 2868b28..e01890f 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml @@ -271,7 +271,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "pyarrow" git: @@ -301,7 +301,7 @@ build_info: output: "target/nextflow/convert/from_cells2stats_to_h5mu" executable: "target/nextflow/convert/from_cells2stats_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf index 83faeb2..c790e7d 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf @@ -3357,7 +3357,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "anndata<0.11.0", + "anndata~=0.11.1", "mudata~=0.3.1", "pyarrow" ], @@ -3399,7 +3399,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml index 8216fb5..cd65f40 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -199,11 +199,11 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "spatialdata~=0.5.0" - "pyarrow~=18.0.0" - - "squidpy<1.5.0" + - "squidpy~=1.6.5" - "pyarrow" git: - "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" @@ -230,7 +230,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" script: - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ @@ -247,7 +247,7 @@ build_info: output: "target/nextflow/convert/from_cosmx_to_h5mu" executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf index 7cb5c57..4bf6ab4 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf @@ -3295,11 +3295,11 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "anndata<0.11.0", + "anndata~=0.11.1", "mudata~=0.3.1", "spatialdata~=0.5.0", "pyarrow~=18.0.0", - "squidpy<1.5.0", + "squidpy~=1.6.5", "pyarrow" ], "git" : [ @@ -3341,7 +3341,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "anndata<0.11.0", + "anndata~=0.11.1", "mudata~=0.3.1" ], "script" : [ @@ -3362,7 +3362,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3501,12 +3501,26 @@ def main(): logger.info("Reading in CosMx data...") input_files = retrieve_input_data(par["input"]) - adata = sq.read.nanostring( - path=input_files["counts_file"].parent, - counts_file=input_files["counts_file"].name, - meta_file=input_files["meta_file"].name, - fov_file=input_files["fov_file"].name, - ) + try: + adata = sq.read.nanostring( + path=input_files["counts_file"].parent, + counts_file=input_files["counts_file"].name, + meta_file=input_files["meta_file"].name, + fov_file=input_files["fov_file"].name, + ) + except ValueError as e: + if "Index fov invalid" in str(e): + import pandas as pd + df = pd.read_csv(input_files["fov_file"]) + df.rename(columns={"FOV": "fov"}, inplace=True) + df.to_csv(input_files["fov_file"], index=False) + + adata = sq.read.nanostring( + path=input_files["counts_file"].parent, + counts_file=input_files["counts_file"].name, + meta_file=input_files["meta_file"].name, + fov_file=input_files["fov_file"].name, + ) logger.info("Writing output MuData object...") mdata = mu.MuData({par["modality"]: adata}) diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index 335e6f7..bc9c878 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -234,7 +234,7 @@ build_info: output: "target/nextflow/convert/from_cosmx_to_spatialexperiment" executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf index 65ee5e5..2a6f66b 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf @@ -3326,7 +3326,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml index eca4f02..87e46c2 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml @@ -207,7 +207,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" script: - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ @@ -224,7 +224,7 @@ build_info: output: "target/nextflow/convert/from_h5mu_to_spatialexperiment" executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf index 4b60d4a..6a6c8d4 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf @@ -3311,7 +3311,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "anndata<0.11.0", + "anndata~=0.11.1", "mudata~=0.3.1" ], "script" : [ @@ -3332,7 +3332,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index c917cf0..4749a75 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -190,7 +190,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "spatialdata~=0.5.0" - "pyarrow~=18.0.0" @@ -221,7 +221,7 @@ build_info: output: "target/nextflow/convert/from_spatialdata_to_h5mu" executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf index 68ad304..2a5ec35 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf @@ -3288,7 +3288,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "anndata<0.11.0", + "anndata~=0.11.1", "mudata~=0.3.1", "spatialdata~=0.5.0", "pyarrow~=18.0.0" @@ -3331,7 +3331,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml index 03471f1..bdb2eff 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml @@ -213,7 +213,7 @@ engines: - type: "python" user: false packages: - - "anndata<0.11.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" - "scanpy~=1.10.4" - "pyarrow" @@ -244,7 +244,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_h5mu" executable: "target/nextflow/convert/from_xenium_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_xenium_to_h5mu/main.nf b/target/nextflow/convert/from_xenium_to_h5mu/main.nf index 4d71a1f..9bf56c9 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf +++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf @@ -3305,7 +3305,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "anndata<0.11.0", + "anndata~=0.11.1", "mudata~=0.3.1", "scanpy~=1.10.4", "pyarrow" @@ -3348,7 +3348,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml index 41d21ea..2b5e0e1 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -326,7 +326,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_spatialdata" executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf index 154e1a7..a91a862 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf @@ -3443,7 +3443,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 27a4caa..ac0d56a 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -224,7 +224,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_spatialexperiment" executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf index 2ca9bc9..8533f55 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf @@ -3315,7 +3315,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml index e86219b..e86b1c8 100644 --- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml @@ -426,7 +426,7 @@ build_info: output: "target/nextflow/mapping/spaceranger_count" executable: "target/nextflow/mapping/spaceranger_count/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf index bd183fb..269871c 100644 --- a/target/nextflow/mapping/spaceranger_count/main.nf +++ b/target/nextflow/mapping/spaceranger_count/main.nf @@ -3548,7 +3548,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml index 6e1c784..992fec9 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml @@ -640,7 +640,7 @@ build_info: output: "target/nextflow/workflows/multiomics/spatial_process_samples" executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples" diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf index 856c9a0..9921f8f 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf @@ -3807,7 +3807,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml index 9d7089e..a9aae92 100644 --- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml +++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml @@ -387,7 +387,7 @@ build_info: output: "target/nextflow/workflows/qc/spatial_qc" executable: "target/nextflow/workflows/qc/spatial_qc/main.nf" viash_version: "0.9.4" - git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763" + git_commit: "6ac22db1075448735626eea2860ab5f3cd022348" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc" diff --git a/target/nextflow/workflows/qc/spatial_qc/main.nf b/target/nextflow/workflows/qc/spatial_qc/main.nf index 7bfa959..fea94a1 100644 --- a/target/nextflow/workflows/qc/spatial_qc/main.nf +++ b/target/nextflow/workflows/qc/spatial_qc/main.nf @@ -3505,7 +3505,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc", "viash_version" : "0.9.4", - "git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763", + "git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : {