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Merge branch 'refs/heads/devel'
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@sunset666
sunset666 committed Aug 7, 2024
2 parents 516b136 + a16a968 commit 54d1997
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3 changes: 3 additions & 0 deletions .gitmodules
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[submodule "src/ingest-pipeline/airflow/dags/cwl/deepcelltypes"]
path = src/ingest-pipeline/airflow/dags/cwl/deepcelltypes
url = https://github.com/hubmapconsortium/deepcelltypes
[submodule "src/ingest-pipeline/airflow/dags/cwl/phenocycler-pipeline"]
path = src/ingest-pipeline/airflow/dags/cwl/phenocycler-pipeline
url = https://github.com/hubmapconsortium/phenocycler-pipeline
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/codex-pipeline
Submodule codex-pipeline updated 13 files
+103 −8 bin/convert_to_ometiff.py
+22 −4 bin/dataset_info/collect_dataset_info_old.py
+0 −1 environment.yml
+1 −1 steps/illumination_first_stitching/best_focus.cwl
+1 −1 steps/illumination_first_stitching/collect_dataset_info.cwl
+1 −1 steps/illumination_first_stitching/create_yaml_config.cwl
+1 −1 steps/illumination_first_stitching/first_stitching.cwl
+1 −1 steps/illumination_first_stitching/illumination_correction.cwl
+1 −1 steps/illumination_first_stitching/slicing.cwl
+1 −1 steps/ometiff_second_stitching/background_subtraction.cwl
+1 −1 steps/ometiff_second_stitching/ome_tiff_creation.cwl
+1 −1 steps/ometiff_second_stitching/second_stitching.cwl
+1 −1 steps/run_cytokit.cwl
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/multiome-rna-atac-pipeline
Submodule multiome-rna-atac-pipeline updated 7 files
+6 −4 bin/downstream.py
+19 −1 pipeline-manifest.json
+57 −4 pipeline.cwl
+1 −1 salmon-rnaseq
+1 −1 sc-atac-seq-pipeline
+2 −2 steps/consolidate_counts.cwl
+3 −3 steps/downstream.cwl
1 change: 1 addition & 0 deletions src/ingest-pipeline/airflow/dags/cwl/phenocycler-pipeline
Submodule phenocycler-pipeline added at 1e3521
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq
Submodule salmon-rnaseq updated 17 files
+16 −6 bin/analysis/compute_qc_metrics.py
+1 −0 docker/analysis/requirements.txt
+2 −2 pipeline.cwl
+1 −1 steps/bulk-salmon-mouse.cwl
+1 −1 steps/bulk-salmon.cwl
+3 −3 steps/compute-qc-metrics.cwl
+1 −1 steps/expression-matrix.cwl
+1 −1 steps/fastqc.cwl
+1 −1 steps/salmon-quantification/adjust-barcodes.cwl
+1 −1 steps/salmon-quantification/alevin-to-anndata.cwl
+1 −1 steps/salmon-quantification/annotate-cells.cwl
+1 −1 steps/salmon-quantification/salmon-mouse.cwl
+1 −1 steps/salmon-quantification/salmon.cwl
+1 −1 steps/salmon-quantification/trim-reads.cwl
+1 −1 steps/scanpy-analysis.cwl
+1 −1 steps/scvelo-analysis.cwl
+1 −1 steps/squidpy-analysis.cwl
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/sc-atac-seq-pipeline
Submodule sc-atac-seq-pipeline updated 19 files
+1 −1 bulk_gather_sequence_bundles.cwl
+13 −0 sc_atac_seq_prep_process_analyze.cwl
+1 −1 steps/adjust-barcodes.cwl
+1 −1 steps/align_reads.cwl
+1 −1 steps/call_peaks.cwl
+1 −1 steps/concat-fastq.cwl
+1 −1 steps/convert_to_h5ad.cwl
+1 −1 steps/fastqc.cwl
+1 −1 steps/index_merged_bam.cwl
+1 −1 steps/merge_bam.cwl
+1 −1 steps/motif_and_tf_analysis.cwl
+1 −1 steps/qc_measures.cwl
+1 −1 steps/sc_atac_seq_analyze_steps/archr_clustering.cwl
+1 −1 steps/sc_atac_seq_analyze_steps/archr_fundamental.cwl
+1 −1 steps/sc_atac_seq_analyze_steps/archr_init_analyze.cwl
+1 −1 steps/sc_atac_seq_process_steps/create_fragment_file.cwl
+1 −1 steps/sc_atac_seq_process_steps/remove_blacklist.cwl
+1 −1 steps/sc_atac_seq_process_steps/sort_bam_file_tool.cwl
+1 −1 steps/write_genome_build.cwl
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