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CI: Fix scGPT Annotation integration test dependencies (#928) #1128

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Job	Run time
Build and push target folder	6m 12s
celltypist - annotate - Build and push docker image	2m 13s
onclass - annotate - Build and push docker image	11m 11s
popv - annotate - Build and push docker image	12m 9s
random_forest_annotation - annotate - Build and push docker image	1m 57s
scanvi - annotate - Build and push docker image	9m 38s
svm_annotation - annotate - Build and push docker image	1m 25s
leiden - cluster - Build and push docker image	1m 48s
compress_h5mu - compression - Build and push docker image	1m 41s
tar_extract - compression - Build and push docker image	1m 57s
from_10xh5_to_h5mu - convert - Build and push docker image	1m 58s
from_10xmtx_to_h5mu - convert - Build and push docker image	1m 50s
from_bd_to_10x_molecular_barcode_tags - convert - Build and push docker image	55s
from_bdrhap_to_h5mu - convert - Build and push docker image	1m 23s
from_cellranger_multi_to_h5mu - convert - Build and push docker image	2m 11s
from_h5ad_to_h5mu - convert - Build and push docker image	2m 17s
from_h5mu_to_h5ad - convert - Build and push docker image	1m 18s
from_h5mu_to_seurat - convert - Build and push docker image	3m 30s
cellbender_remove_background - correction - Build and push docker image	11m 40s
cellbender_remove_background_v0_2 - correction - Build and push docker image	6m 35s
concatenate_h5mu - dataflow - Build and push docker image	1m 18s
merge - dataflow - Build and push docker image	1m 13s
split_h5mu - dataflow - Build and push docker image	1m 17s
split_h5mu_train_test - dataflow - Build and push docker image	2m 25s
split_modalities - dataflow - Build and push docker image	1m 12s
bcl2fastq - demux - Build and push docker image	57s
bcl_convert - demux - Build and push docker image	1m 3s
cellranger_atac_mkfastq - demux - Build and push docker image	2m 36s
cellranger_mkfastq - demux - Build and push docker image	1m 38s
densmap - dimred - Build and push docker image	1m 36s
lsi - dimred - Build and push docker image	2m 3s
pca - dimred - Build and push docker image	3m 8s
tsne - dimred - Build and push docker image	2m 30s
umap - dimred - Build and push docker image	2m 1s
download_file - download - Build and push docker image	2m 16s
sync_test_resources - download - Build and push docker image	54s
highly_variable_features_scanpy - feature_annotation - Build and push docker image	2m 0s
score_genes_cell_cycle_scanpy - feature_annotation - Build and push docker image	1m 58s
score_genes_scanpy - feature_annotation - Build and push docker image	1m 59s
make_params - files - Build and push docker image	1m 28s
delimit_fraction - filter - Build and push docker image	1m 16s
do_filter - filter - Build and push docker image	1m 13s
filter_with_counts - filter - Build and push docker image	2m 25s
filter_with_scrublet - filter - Build and push docker image	2m 3s
intersect_obs - filter - Build and push docker image	1m 17s
remove_modality - filter - Build and push docker image	1m 20s
subset_h5mu - filter - Build and push docker image	1m 25s
subset_obsp - filter - Build and push docker image	1m 21s
bcftools - genetic_demux - Build and push docker image	4m 23s
cellsnp - genetic_demux - Build and push docker image	2m 35s
demuxlet - genetic_demux - Build and push docker image	7m 9s
dsc_pileup - genetic_demux - Build and push docker image	4m 27s
freebayes - genetic_demux - Build and push docker image	1m 6s
freemuxlet - genetic_demux - Build and push docker image	8m 26s
samtools - genetic_demux - Build and push docker image	3m 57s
scsplit - genetic_demux - Build and push docker image	2m 15s
souporcell - genetic_demux - Build and push docker image	2m 12s
vireo - genetic_demux - Build and push docker image	2m 41s
harmonypy - integrate - Build and push docker image	1m 52s
scanorama - integrate - Build and push docker image	4m 5s
scarches - integrate - Build and push docker image	13m 43s
scvi - integrate - Build and push docker image	15m 1s
totalvi - integrate - Build and push docker image	14m 58s
lianapy - interpret - Build and push docker image	1m 55s
knn - labels_transfer - Build and push docker image	1m 37s
xgboost - labels_transfer - Build and push docker image	2m 31s
bd_rhapsody - mapping - Build and push docker image	2m 8s
cellranger_atac_count - mapping - Build and push docker image	1m 11s
cellranger_count - mapping - Build and push docker image	1m 25s
cellranger_count_split - mapping - Build and push docker image	2m 4s
cellranger_multi - mapping - Build and push docker image	1m 42s
htseq_count - mapping - Build and push docker image	1m 20s
htseq_count_to_h5mu - mapping - Build and push docker image	1m 44s
multi_star - mapping - Build and push docker image	5m 21s
multi_star_to_h5mu - mapping - Build and push docker image	2m 15s
samtools_sort - mapping - Build and push docker image	55s
star_align - mapping - Build and push docker image	5m 38s
star_align_v273a - mapping - Build and push docker image	3m 10s
add_id - metadata - Build and push docker image	2m 23s
duplicate_obs - metadata - Build and push docker image	2m 24s
duplicate_var - metadata - Build and push docker image	2m 45s
grep_annotation_column - metadata - Build and push docker image	2m 30s
join_csv - metadata - Build and push docker image	1m 18s
join_uns_to_obs - metadata - Build and push docker image	1m 17s
move_obsm_to_obs - metadata - Build and push docker image	2m 15s
bbknn - neighbors - Build and push docker image	4m 34s
find_neighbors - neighbors - Build and push docker image	1m 51s
filter_10xh5 - process_10xh5 - Build and push docker image	3m 8s
calculate_qc_metrics - qc - Build and push docker image	2m 41s
fastqc - qc - Build and push docker image	2m 55s
multiqc - qc - Build and push docker image	3m 7s
cellxgene_census - query - Build and push docker image	3m 36s
build_bdrhap_reference - reference - Build and push docker image	1m 38s
build_cellranger_arc_reference - reference - Build and push docker image	2m 56s
build_cellranger_reference - reference - Build and push docker image	2m 54s
build_star_reference - reference - Build and push docker image	3m 50s
cellranger_mkgtf - reference - Build and push docker image	1m 27s
make_reference - reference - Build and push docker image	1m 8s
mermaid - report - Build and push docker image	3m 51s
binning - scgpt - Build and push docker image	2m 17s
cell_type_annotation - scgpt - Build and push docker image	6m 28s
cross_check_genes - scgpt - Build and push docker image	6m 40s
embedding - scgpt - Build and push docker image	7m 42s
pad_tokenize - scgpt - Build and push docker image	7m 23s
publish - transfer - Build and push docker image	42s
bpcells_regress_out - transform - Build and push docker image	9m 48s
clr - transform - Build and push docker image	3m 13s
delete_layer - transform - Build and push docker image	1m 25s
log1p - transform - Build and push docker image	3m 11s
move_layer - transform - Build and push docker image	1m 19s
normalize_total - transform - Build and push docker image	1m 59s
regress_out - transform - Build and push docker image	1m 47s
scale - transform - Build and push docker image	3m 10s
tfidf - transform - Build and push docker image	2m 56s
scvelo - velocity - Build and push docker image	12m 0s
velocyto - velocity - Build and push docker image	2m 48s
velocyto_to_h5mu - convert - Build and push docker image	2m 6s
	6h 26m 48s

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CI: Fix scGPT Annotation integration test dependencies (#928) #1128

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CI: Fix scGPT Annotation integration test dependencies (#928) #1128

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