Build

Cell type annotation: scGPT workflow (#832) #1122

Run time

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Job	Run time
Build and push target folder	5m 55s
celltypist - annotate - Build and push docker image	3m 32s
onclass - annotate - Build and push docker image	18m 8s
popv - annotate - Build and push docker image	11m 36s
random_forest_annotation - annotate - Build and push docker image	1m 25s
scanvi - annotate - Build and push docker image	9m 36s
svm_annotation - annotate - Build and push docker image	2m 45s
leiden - cluster - Build and push docker image	2m 20s
compress_h5mu - compression - Build and push docker image	2m 13s
tar_extract - compression - Build and push docker image	53s
from_10xh5_to_h5mu - convert - Build and push docker image	2m 2s
from_10xmtx_to_h5mu - convert - Build and push docker image	1m 57s
from_bd_to_10x_molecular_barcode_tags - convert - Build and push docker image	1m 1s
from_bdrhap_to_h5mu - convert - Build and push docker image	2m 52s
from_cellranger_multi_to_h5mu - convert - Build and push docker image	2m 7s
from_h5ad_to_h5mu - convert - Build and push docker image	1m 20s
from_h5mu_to_h5ad - convert - Build and push docker image	2m 47s
from_h5mu_to_seurat - convert - Build and push docker image	2m 8s
cellbender_remove_background - correction - Build and push docker image	11m 2s
cellbender_remove_background_v0_2 - correction - Build and push docker image	5m 19s
concatenate_h5mu - dataflow - Build and push docker image	1m 27s
merge - dataflow - Build and push docker image	2m 30s
split_h5mu - dataflow - Build and push docker image	2m 11s
split_h5mu_train_test - dataflow - Build and push docker image	3m 13s
split_modalities - dataflow - Build and push docker image	1m 19s
bcl2fastq - demux - Build and push docker image	1m 58s
bcl_convert - demux - Build and push docker image	54s
cellranger_atac_mkfastq - demux - Build and push docker image	1m 14s
cellranger_mkfastq - demux - Build and push docker image	1m 19s
densmap - dimred - Build and push docker image	3m 20s
lsi - dimred - Build and push docker image	3m 31s
pca - dimred - Build and push docker image	3m 1s
tsne - dimred - Build and push docker image	3m 46s
umap - dimred - Build and push docker image	3m 43s
download_file - download - Build and push docker image	45s
sync_test_resources - download - Build and push docker image	55s
highly_variable_features_scanpy - feature_annotation - Build and push docker image	3m 3s
score_genes_cell_cycle_scanpy - feature_annotation - Build and push docker image	2m 8s
score_genes_scanpy - feature_annotation - Build and push docker image	2m 32s
make_params - files - Build and push docker image	2m 17s
delimit_fraction - filter - Build and push docker image	2m 27s
do_filter - filter - Build and push docker image	2m 38s
filter_with_counts - filter - Build and push docker image	2m 47s
filter_with_scrublet - filter - Build and push docker image	3m 16s
intersect_obs - filter - Build and push docker image	1m 13s
remove_modality - filter - Build and push docker image	1m 25s
subset_h5mu - filter - Build and push docker image	2m 45s
subset_obsp - filter - Build and push docker image	1m 13s
bcftools - genetic_demux - Build and push docker image	2m 36s
cellsnp - genetic_demux - Build and push docker image	2m 41s
demuxlet - genetic_demux - Build and push docker image	5m 59s
dsc_pileup - genetic_demux - Build and push docker image	4m 18s
freebayes - genetic_demux - Build and push docker image	1m 21s
freemuxlet - genetic_demux - Build and push docker image	7m 2s
samtools - genetic_demux - Build and push docker image	4m 1s
scsplit - genetic_demux - Build and push docker image	1m 45s
souporcell - genetic_demux - Build and push docker image	2m 11s
vireo - genetic_demux - Build and push docker image	3m 50s
harmonypy - integrate - Build and push docker image	2m 13s
scanorama - integrate - Build and push docker image	2m 34s
scarches - integrate - Build and push docker image	14m 21s
scvi - integrate - Build and push docker image	14m 47s
totalvi - integrate - Build and push docker image	12m 59s
lianapy - interpret - Build and push docker image	1m 56s
knn - labels_transfer - Build and push docker image	3m 18s
xgboost - labels_transfer - Build and push docker image	4m 0s
bd_rhapsody - mapping - Build and push docker image	2m 56s
cellranger_atac_count - mapping - Build and push docker image	2m 27s
cellranger_count - mapping - Build and push docker image	1m 24s
cellranger_count_split - mapping - Build and push docker image	1m 51s
cellranger_multi - mapping - Build and push docker image	3m 28s
htseq_count - mapping - Build and push docker image	2m 26s
htseq_count_to_h5mu - mapping - Build and push docker image	1m 29s
multi_star - mapping - Build and push docker image	5m 34s
multi_star_to_h5mu - mapping - Build and push docker image	1m 20s
samtools_sort - mapping - Build and push docker image	2m 18s
star_align - mapping - Build and push docker image	3m 57s
star_align_v273a - mapping - Build and push docker image	3m 4s
add_id - metadata - Build and push docker image	1m 23s
duplicate_obs - metadata - Build and push docker image	1m 17s
duplicate_var - metadata - Build and push docker image	2m 5s
grep_annotation_column - metadata - Build and push docker image	1m 20s
join_csv - metadata - Build and push docker image	1m 21s
join_uns_to_obs - metadata - Build and push docker image	2m 50s
move_obsm_to_obs - metadata - Build and push docker image	1m 20s
bbknn - neighbors - Build and push docker image	2m 52s
find_neighbors - neighbors - Build and push docker image	1m 51s
filter_10xh5 - process_10xh5 - Build and push docker image	2m 20s
calculate_qc_metrics - qc - Build and push docker image	1m 17s
fastqc - qc - Build and push docker image	3m 19s
multiqc - qc - Build and push docker image	2m 10s
cellxgene_census - query - Build and push docker image	3m 46s
build_bdrhap_reference - reference - Build and push docker image	1m 41s
build_cellranger_arc_reference - reference - Build and push docker image	1m 25s
build_cellranger_reference - reference - Build and push docker image	2m 42s
build_star_reference - reference - Build and push docker image	3m 34s
cellranger_mkgtf - reference - Build and push docker image	2m 44s
make_reference - reference - Build and push docker image	2m 3s
mermaid - report - Build and push docker image	3m 33s
binning - scgpt - Build and push docker image	2m 38s
cell_type_annotation - scgpt - Build and push docker image	6m 49s
cross_check_genes - scgpt - Build and push docker image	6m 37s
embedding - scgpt - Build and push docker image	6m 25s
pad_tokenize - scgpt - Build and push docker image	6m 17s
publish - transfer - Build and push docker image	43s
bpcells_regress_out - transform - Build and push docker image	10m 23s
clr - transform - Build and push docker image	2m 43s
delete_layer - transform - Build and push docker image	1m 16s
log1p - transform - Build and push docker image	1m 59s
move_layer - transform - Build and push docker image	1m 19s
normalize_total - transform - Build and push docker image	3m 12s
regress_out - transform - Build and push docker image	3m 9s
scale - transform - Build and push docker image	2m 27s
tfidf - transform - Build and push docker image	3m 43s
scvelo - velocity - Build and push docker image	9m 36s
velocyto - velocity - Build and push docker image	3m 3s
velocyto_to_h5mu - convert - Build and push docker image	2m 2s
	6h 39m 8s

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Cell type annotation: scGPT workflow (#832) #1122

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Cell type annotation: scGPT workflow (#832) #1122

Jobs

Run details

Run time