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Merge branch 'devel'. Updates to submodules, plus some misc/tools uti…
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…lities.
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@jswelling
jswelling committed Apr 2, 2021
2 parents 09bdead + 495c695 commit 15d92fd
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Showing 12 changed files with 507 additions and 62 deletions.
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/codex-pipeline
Submodule codex-pipeline updated 17 files
+2 −2 codex_stitching/best_z_identification.py
+27 −16 codex_stitching/best_z_paths.py
+130 −0 codex_stitching/directory_management.py
+0 −10 codex_stitching/file_manipulation.py
+3 −3 codex_stitching/generate_bigstitcher_macro.py
+6 −31 codex_stitching/image_path_arrangement.py
+159 −0 codex_stitching/image_stitching.py
+130 −0 codex_stitching/run_stitching.py
+405 −0 codex_stitching/secondary_stitcher/mask_stitching.py
+80 −253 codex_stitching/secondary_stitcher/secondary_stitcher.py
+0 −383 codex_stitching/stitch.py
+1 −1 steps/collect_dataset_info.cwl
+1 −1 steps/create_yaml_config.cwl
+2 −2 steps/first_stitching.cwl
+1 −1 steps/ome_tiff_creation.cwl
+1 −1 steps/run_cytokit.cwl
+1 −1 steps/second_stitching.cwl
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/portal-containers
Submodule portal-containers updated 66 files
+2 −2 anndata-to-ui-manifest.json
+1 −1 anndata-to-ui.cwl
+1 −1 containers/anndata-to-ui/VERSION
+26 −9 containers/anndata-to-ui/context/main.py
+1 −1 containers/anndata-to-ui/context/requirements.txt
+17 −7 containers/anndata-to-ui/create-test-input.py
+ − containers/anndata-to-ui/test-input/scvelo_annotated.h5ad
+ − containers/anndata-to-ui/test-input/secondary_analysis.h5ad
+3 −0 containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/.zgroup
+8 −0 containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/.zattrs
+3 −0 containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/.zgroup
+20 −0 containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/data/.zarray
+ − containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/data/0
+20 −0 containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/indices/.zarray
+ − containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/indices/0
+20 −0 containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/indptr/.zarray
+ − containers/anndata-to-ui/test-output-expected/scvelo_annotated.zarr/layers/spliced/indptr/0
+1 −1 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/X/.zarray
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/X/0.0
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/X/0.1
+3 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/.zgroup
+22 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/scaled/.zarray
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/scaled/0.0
+8 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/.zattrs
+3 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/.zgroup
+20 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/data/.zarray
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/data/0
+20 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/indices/.zarray
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/indices/0
+20 −0 containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/indptr/.zarray
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/layers/unscaled/indptr/0
+ − containers/anndata-to-ui/test-output-expected/secondary_analysis.zarr/var/top_highly_variable/0
+1 −1 containers/sprm-to-anndata/VERSION
+1 −1 containers/sprm-to-anndata/context/main.py
+0 −2 containers/sprm-to-anndata/test-output-expected/R001_X001_Y001-anndata.zarr/obsm/xy/.zarray
+ − containers/sprm-to-anndata/test-output-expected/R001_X001_Y001-anndata.zarr/obsm/xy/0.0
+1 −1 sprm-to-anndata-manifest.json
+1 −1 sprm-to-anndata.cwl
+ − workflows/anndata-to-ui/test-input/scvelo_annotated.h5ad
+ − workflows/anndata-to-ui/test-input/secondary_analysis.h5ad
+3 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/.zgroup
+8 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/.zattrs
+3 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/.zgroup
+20 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/data/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/data/0
+20 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/indices/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/indices/0
+20 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/indptr/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/scvelo_annotated.zarr/layers/spliced/indptr/0
+1 −1 workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/X/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/X/0.0
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/X/0.1
+3 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/.zgroup
+22 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/scaled/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/scaled/0.0
+8 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/.zattrs
+3 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/.zgroup
+20 −0 workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/data/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/data/0
+20 −0 ...ows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/indices/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/indices/0
+20 −0 ...lows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/indptr/.zarray
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/layers/unscaled/indptr/0
+ − workflows/anndata-to-ui/test-output-expected/anndata-zarr/secondary_analysis.zarr/var/top_highly_variable/0
+0 −2 workflows/sprm-to-anndata/test-output-expected/anndata-zarr/R001_X001_Y001-anndata.zarr/obsm/xy/.zarray
+ − workflows/sprm-to-anndata/test-output-expected/anndata-zarr/R001_X001_Y001-anndata.zarr/obsm/xy/0.0
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq
Submodule salmon-rnaseq updated 11 files
+2 −0 bin/analysis/scanpy_entry_point.py
+56 −5 bin/common/common.py
+1 −1 steps/adjust-barcodes.cwl
+1 −1 steps/alevin-to-anndata.cwl
+1 −1 steps/annotate-cells.cwl
+1 −1 steps/bulk-salmon.cwl
+1 −1 steps/expression-matrix.cwl
+1 −1 steps/fastqc.cwl
+1 −1 steps/salmon.cwl
+1 −1 steps/scanpy-analysis.cwl
+1 −1 steps/scvelo-analysis.cwl
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/sprm
Submodule sprm updated 8 files
+3 −1 README.md
+1 −0 setup.py
+1 −1 sprm/SPRM.py
+7 −4 sprm/SPRM_pkg.py
+1 −0 sprm/options.txt
+21 −9 sprm/outlinePCA.py
+1 −1 sprm/version.txt
+1 −1 steps/sprm.cwl
8 changes: 7 additions & 1 deletion src/ingest-pipeline/airflow/dags/salmon_rnaseq.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -320,9 +320,15 @@ def get_salmon_dag_params(assay: str) -> SequencingDagParameters:
SequencingDagParameters(
dag_id="salmon_rnaseq_10x",
pipeline_name="salmon-rnaseq",
assay="10x",
assay="10x_v3",
dataset_type="salmon_rnaseq_10x",
),
SequencingDagParameters(
dag_id="salmon_rnaseq_10x_sn",
pipeline_name="salmon-rnaseq",
assay="10x_v3_sn",
dataset_type="salmon_rnaseq_10x_sn",
),
get_salmon_dag_params("sciseq"),
get_salmon_dag_params("slideseq"),
get_salmon_dag_params("snareseq"),
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1 change: 1 addition & 0 deletions src/ingest-pipeline/airflow/dags/sc_atac_seq.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@ def build_cwltool_cmd1(**kwargs):

command = [
*get_cwltool_base_cmd(tmpdir),
cwl_workflows[0],
"--assay",
params.assay,
"--outdir",
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2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/workflow_map.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ workflow_map:
'workflow': 'sc_atac_seq_sn'
- 'collection_type': 'generic_metadatatsv'
'assay_type': 'snRNAseq'
'workflow': 'salmon_rnaseq_10x'
'workflow': 'salmon_rnaseq_10x_sn'
- 'collection_type': 'bulkatacseq_collection'
'assay_type': 'ATACseq-bulk'
'workflow': 'bulk_atacseq'
Expand Down
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