From 45dd0704ac112eebbf151f13a11c40ba5d22e579 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 23 Mar 2026 19:38:01 +0000 Subject: [PATCH 1/3] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black-pre-commit-mirror: 26.3.0 → 26.3.1](https://github.com/psf/black-pre-commit-mirror/compare/26.3.0...26.3.1) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8069507..71db723 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,7 +26,7 @@ repos: # https://github.com/codespell-project/codespell/issues/1498 # Python formatting - repo: https://github.com/psf/black-pre-commit-mirror - rev: 26.3.0 + rev: 26.3.1 hooks: - id: black # R formatting From a64b03cfa7dd7cfe2369fd375168de11ea200d9b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 23 Mar 2026 19:39:27 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/params.md | 115 +++++++++++++++++++++++-------------------------- 1 file changed, 54 insertions(+), 61 deletions(-) diff --git a/docs/params.md b/docs/params.md index 77a4744..fb74aee 100644 --- a/docs/params.md +++ b/docs/params.md @@ -6,83 +6,76 @@ SINgle CelL AnalysIs Resource Define where the pipeline should find input data and save output data. -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `input` | Path to CSV file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row.
| `string` | assets/input_manifest.csv | True | | -| `contrast` | Path to CSV file with contrast specification | `string` | assets/contrast_manifest.csv | True | | -| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | results | True | | -| `run_cellranger` | whether to run cellranger | `boolean` | True | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ---------------------------- | -------- | ------ | +| `input` | Path to CSV file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row.
| `string` | assets/input_manifest.csv | True | | +| `contrast` | Path to CSV file with contrast specification | `string` | assets/contrast_manifest.csv | True | | +| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | results | True | | +| `run_cellranger` | whether to run cellranger | `boolean` | True | | | ## Main options - - -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `species` | | `string` | hg19 | | | -| `vars_to_regress` | | `string` | | | | -| `qc_filtering` | | `string` | manual | | | -| `nCount_RNA_max` | | `integer` | 500000 | | | -| `nCount_RNA_min` | | `integer` | 1000 | | | -| `nFeature_RNA_max` | | `integer` | 5000 | | | -| `nFeature_RNA_min` | | `integer` | 200 | | | -| `percent_mt_max` | | `integer` | 10 | | | -| `percent_mt_min` | | `integer` | 0 | | | -| `run_doublet_finder` | (accepted: `Y`\|`N`) | `string` | Y | | | -| `seurat_resolution` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | -| `npcs` | | `integer` | 50 | | | -| `resolution_list` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | -| `save_cellranger_extra_files` | Whether to save extra cellranger files (bam, bai, cloupe) in addition to h5 files | `boolean` | False | | | -| `genome_dir` | Path to the genome references. Overridden by platform configs, e.g. conf/biowulf.config | `string` | | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ----------------------------- | --------------------------------------------------------------------------------------- | --------- | ------------------------- | -------- | ------ | +| `species` | | `string` | hg19 | | | +| `vars_to_regress` | | `string` | | | | +| `qc_filtering` | | `string` | manual | | | +| `nCount_RNA_max` | | `integer` | 500000 | | | +| `nCount_RNA_min` | | `integer` | 1000 | | | +| `nFeature_RNA_max` | | `integer` | 5000 | | | +| `nFeature_RNA_min` | | `integer` | 200 | | | +| `percent_mt_max` | | `integer` | 10 | | | +| `percent_mt_min` | | `integer` | 0 | | | +| `run_doublet_finder` | (accepted: `Y`\|`N`) | `string` | Y | | | +| `seurat_resolution` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | +| `npcs` | | `integer` | 50 | | | +| `resolution_list` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | +| `save_cellranger_extra_files` | Whether to save extra cellranger files (bam, bai, cloupe) in addition to h5 files | `boolean` | False | | | +| `genome_dir` | Path to the genome references. Overridden by platform configs, e.g. conf/biowulf.config | `string` | | | | ## Institutional config options - - -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `config_profile_name` | | `string` | | | | -| `config_profile_description` | | `string` | | | | -| `config_profile_contact` | | `string` | | | | -| `config_profile_url` | | `string` | | | | +| Parameter | Description | Type | Default | Required | Hidden | +| ---------------------------- | ----------- | -------- | ------- | -------- | ------ | +| `config_profile_name` | | `string` | | | | +| `config_profile_description` | | `string` | | | | +| `config_profile_contact` | | `string` | | | | +| `config_profile_url` | | `string` | | | | ## Generic options - - -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `publish_dir_mode` | | `string` | link | True | | -| `tracedir` | | `string` | ${params.outdir}/pipeline_info | True | | -| `max_memory` | | `string` | 128.GB | True | | -| `max_cpus` | | `integer` | 48 | True | | -| `max_time` | | `string` | 240.h | True | | +| Parameter | Description | Type | Default | Required | Hidden | +| ------------------ | ----------- | --------- | ------------------------------ | -------- | ------ | +| `publish_dir_mode` | | `string` | link | True | | +| `tracedir` | | `string` | ${params.outdir}/pipeline_info | True | | +| `max_memory` | | `string` | 128.GB | True | | +| `max_cpus` | | `integer` | 48 | True | | +| `max_time` | | `string` | 240.h | True | | ## Containers Docker/Singularity containers to use for processes. Must be available in dockerhub -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `base_container` | | `string` | nciccbr/ccbr_ubuntu_base_20.04:v6.1 | | True | -| `baser_container` | | `string` | nciccbr/sinclair_baser:0.1.0 | | True | +| Parameter | Description | Type | Default | Required | Hidden | +| ----------------- | ----------- | -------- | ----------------------------------- | -------- | ------ | +| `base_container` | | `string` | nciccbr/ccbr_ubuntu_base_20.04:v6.1 | | True | +| `baser_container` | | `string` | nciccbr/sinclair_baser:0.1.0 | | True | ## Hidden options +| Parameter | Description | Type | Default | Required | Hidden | +| ----------------------- | ----------- | -------- | ------------------------------------------------------- | -------- | ------ | +| `Rlib_dir` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_scRNA_RHEL8 | | True | +| `conda_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env | | True | +| `python_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env/bin | | True | +| `Rpkg` | | `string` | ${projectDir}/conf/Rpack.config | | True | +| `script_functions` | | `string` | ${projectDir}/bin/scRNA_functions.R | | True | +| `script_preprocess` | | `string` | ${projectDir}/bin/seurat_preprocess.Rmd | | True | +| `script_merge` | | `string` | ${projectDir}/bin/seurat_merge.Rmd | | True | +| `script_bc_harmony` | | `string` | ${projectDir}/bin/batch_correction_harmony.Rmd | | True | +| `script_bc_rpca` | | `string` | ${projectDir}/bin/batch_correction_rpca.Rmd | | True | +| `script_bc_cca` | | `string` | ${projectDir}/bin/batch_correction_cca.Rmd | | True | +| `script_liger` | | `string` | ${projectDir}/bin/batch_correction_liger.Rmd | | True | +| `script_bc_integration` | | `string` | ${projectDir}/bin/batch_correction_integration.Rmd | | True | - -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `Rlib_dir` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_scRNA_RHEL8 | | True | -| `conda_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env | | True | -| `python_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env/bin | | True | -| `Rpkg` | | `string` | ${projectDir}/conf/Rpack.config | | True | -| `script_functions` | | `string` | ${projectDir}/bin/scRNA_functions.R | | True | -| `script_preprocess` | | `string` | ${projectDir}/bin/seurat_preprocess.Rmd | | True | -| `script_merge` | | `string` | ${projectDir}/bin/seurat_merge.Rmd | | True | -| `script_bc_harmony` | | `string` | ${projectDir}/bin/batch_correction_harmony.Rmd | | True | -| `script_bc_rpca` | | `string` | ${projectDir}/bin/batch_correction_rpca.Rmd | | True | -| `script_bc_cca` | | `string` | ${projectDir}/bin/batch_correction_cca.Rmd | | True | -| `script_liger` | | `string` | ${projectDir}/bin/batch_correction_liger.Rmd | | True | -| `script_bc_integration` | | `string` | ${projectDir}/bin/batch_correction_integration.Rmd | | True | From 791b1d418e466ebcc53363f10e0bd100f5e287a4 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 23 Mar 2026 19:40:39 +0000 Subject: [PATCH 3/3] =?UTF-8?q?ci:=20=F0=9F=93=91=20update=20params=20docs?= =?UTF-8?q?=20with=20'nf-core=20pipelines=20schema=20docs'?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/params.md | 115 ++++++++++++++++++++++++++----------------------- 1 file changed, 61 insertions(+), 54 deletions(-) diff --git a/docs/params.md b/docs/params.md index fb74aee..77a4744 100644 --- a/docs/params.md +++ b/docs/params.md @@ -6,76 +6,83 @@ SINgle CelL AnalysIs Resource Define where the pipeline should find input data and save output data. -| Parameter | Description | Type | Default | Required | Hidden | -| ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ---------------------------- | -------- | ------ | -| `input` | Path to CSV file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row.
| `string` | assets/input_manifest.csv | True | | -| `contrast` | Path to CSV file with contrast specification | `string` | assets/contrast_manifest.csv | True | | -| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | results | True | | -| `run_cellranger` | whether to run cellranger | `boolean` | True | | | +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `input` | Path to CSV file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row.
| `string` | assets/input_manifest.csv | True | | +| `contrast` | Path to CSV file with contrast specification | `string` | assets/contrast_manifest.csv | True | | +| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | results | True | | +| `run_cellranger` | whether to run cellranger | `boolean` | True | | | ## Main options -| Parameter | Description | Type | Default | Required | Hidden | -| ----------------------------- | --------------------------------------------------------------------------------------- | --------- | ------------------------- | -------- | ------ | -| `species` | | `string` | hg19 | | | -| `vars_to_regress` | | `string` | | | | -| `qc_filtering` | | `string` | manual | | | -| `nCount_RNA_max` | | `integer` | 500000 | | | -| `nCount_RNA_min` | | `integer` | 1000 | | | -| `nFeature_RNA_max` | | `integer` | 5000 | | | -| `nFeature_RNA_min` | | `integer` | 200 | | | -| `percent_mt_max` | | `integer` | 10 | | | -| `percent_mt_min` | | `integer` | 0 | | | -| `run_doublet_finder` | (accepted: `Y`\|`N`) | `string` | Y | | | -| `seurat_resolution` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | -| `npcs` | | `integer` | 50 | | | -| `resolution_list` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | -| `save_cellranger_extra_files` | Whether to save extra cellranger files (bam, bai, cloupe) in addition to h5 files | `boolean` | False | | | -| `genome_dir` | Path to the genome references. Overridden by platform configs, e.g. conf/biowulf.config | `string` | | | | + + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `species` | | `string` | hg19 | | | +| `vars_to_regress` | | `string` | | | | +| `qc_filtering` | | `string` | manual | | | +| `nCount_RNA_max` | | `integer` | 500000 | | | +| `nCount_RNA_min` | | `integer` | 1000 | | | +| `nFeature_RNA_max` | | `integer` | 5000 | | | +| `nFeature_RNA_min` | | `integer` | 200 | | | +| `percent_mt_max` | | `integer` | 10 | | | +| `percent_mt_min` | | `integer` | 0 | | | +| `run_doublet_finder` | (accepted: `Y`\|`N`) | `string` | Y | | | +| `seurat_resolution` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | +| `npcs` | | `integer` | 50 | | | +| `resolution_list` | | `string` | 0.1,0.2,0.3,0.5,0.6,0.8,1 | | | +| `save_cellranger_extra_files` | Whether to save extra cellranger files (bam, bai, cloupe) in addition to h5 files | `boolean` | False | | | +| `genome_dir` | Path to the genome references. Overridden by platform configs, e.g. conf/biowulf.config | `string` | | | | ## Institutional config options -| Parameter | Description | Type | Default | Required | Hidden | -| ---------------------------- | ----------- | -------- | ------- | -------- | ------ | -| `config_profile_name` | | `string` | | | | -| `config_profile_description` | | `string` | | | | -| `config_profile_contact` | | `string` | | | | -| `config_profile_url` | | `string` | | | | + + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `config_profile_name` | | `string` | | | | +| `config_profile_description` | | `string` | | | | +| `config_profile_contact` | | `string` | | | | +| `config_profile_url` | | `string` | | | | ## Generic options -| Parameter | Description | Type | Default | Required | Hidden | -| ------------------ | ----------- | --------- | ------------------------------ | -------- | ------ | -| `publish_dir_mode` | | `string` | link | True | | -| `tracedir` | | `string` | ${params.outdir}/pipeline_info | True | | -| `max_memory` | | `string` | 128.GB | True | | -| `max_cpus` | | `integer` | 48 | True | | -| `max_time` | | `string` | 240.h | True | | + + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `publish_dir_mode` | | `string` | link | True | | +| `tracedir` | | `string` | ${params.outdir}/pipeline_info | True | | +| `max_memory` | | `string` | 128.GB | True | | +| `max_cpus` | | `integer` | 48 | True | | +| `max_time` | | `string` | 240.h | True | | ## Containers Docker/Singularity containers to use for processes. Must be available in dockerhub -| Parameter | Description | Type | Default | Required | Hidden | -| ----------------- | ----------- | -------- | ----------------------------------- | -------- | ------ | -| `base_container` | | `string` | nciccbr/ccbr_ubuntu_base_20.04:v6.1 | | True | -| `baser_container` | | `string` | nciccbr/sinclair_baser:0.1.0 | | True | +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `base_container` | | `string` | nciccbr/ccbr_ubuntu_base_20.04:v6.1 | | True | +| `baser_container` | | `string` | nciccbr/sinclair_baser:0.1.0 | | True | ## Hidden options -| Parameter | Description | Type | Default | Required | Hidden | -| ----------------------- | ----------- | -------- | ------------------------------------------------------- | -------- | ------ | -| `Rlib_dir` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_scRNA_RHEL8 | | True | -| `conda_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env | | True | -| `python_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env/bin | | True | -| `Rpkg` | | `string` | ${projectDir}/conf/Rpack.config | | True | -| `script_functions` | | `string` | ${projectDir}/bin/scRNA_functions.R | | True | -| `script_preprocess` | | `string` | ${projectDir}/bin/seurat_preprocess.Rmd | | True | -| `script_merge` | | `string` | ${projectDir}/bin/seurat_merge.Rmd | | True | -| `script_bc_harmony` | | `string` | ${projectDir}/bin/batch_correction_harmony.Rmd | | True | -| `script_bc_rpca` | | `string` | ${projectDir}/bin/batch_correction_rpca.Rmd | | True | -| `script_bc_cca` | | `string` | ${projectDir}/bin/batch_correction_cca.Rmd | | True | -| `script_liger` | | `string` | ${projectDir}/bin/batch_correction_liger.Rmd | | True | -| `script_bc_integration` | | `string` | ${projectDir}/bin/batch_correction_integration.Rmd | | True | + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `Rlib_dir` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_scRNA_RHEL8 | | True | +| `conda_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env | | True | +| `python_path` | | `string` | /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/scvi-env/bin | | True | +| `Rpkg` | | `string` | ${projectDir}/conf/Rpack.config | | True | +| `script_functions` | | `string` | ${projectDir}/bin/scRNA_functions.R | | True | +| `script_preprocess` | | `string` | ${projectDir}/bin/seurat_preprocess.Rmd | | True | +| `script_merge` | | `string` | ${projectDir}/bin/seurat_merge.Rmd | | True | +| `script_bc_harmony` | | `string` | ${projectDir}/bin/batch_correction_harmony.Rmd | | True | +| `script_bc_rpca` | | `string` | ${projectDir}/bin/batch_correction_rpca.Rmd | | True | +| `script_bc_cca` | | `string` | ${projectDir}/bin/batch_correction_cca.Rmd | | True | +| `script_liger` | | `string` | ${projectDir}/bin/batch_correction_liger.Rmd | | True | +| `script_bc_integration` | | `string` | ${projectDir}/bin/batch_correction_integration.Rmd | | True |