diff --git a/src/methods/batchelor_fastmnn/config.vsh.yaml b/src/methods/batchelor_fastmnn/config.vsh.yaml index b5e71c1f..83108b61 100644 --- a/src/methods/batchelor_fastmnn/config.vsh.yaml +++ b/src/methods/batchelor_fastmnn/config.vsh.yaml @@ -11,9 +11,9 @@ description: | 4. Correct the cells in the target batch towards the reference, using locally weighted correction vectors. 5. Merge the corrected target batch with the reference, and repeat with the next target batch. references: - # Haghverdi, L., Lun, A., Morgan, M. et al. - # Batch effects in single-cell RNA-sequencing data are - # corrected by matching mutual nearest neighbors. + # Haghverdi, L., Lun, A., Morgan, M. et al. + # Batch effects in single-cell RNA-sequencing data are + # corrected by matching mutual nearest neighbors. # Nat Biotechnol 36, 421–427 (2018). https://doi.org/10.1038/nbt.4091 doi: 10.1038/nbt.4091 links: @@ -35,4 +35,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowcpu, highmem, midtime] + label: [lowcpu, highmem, hightime] diff --git a/src/methods/batchelor_mnn_correct/config.vsh.yaml b/src/methods/batchelor_mnn_correct/config.vsh.yaml index 6c7f5c21..ff87420b 100644 --- a/src/methods/batchelor_mnn_correct/config.vsh.yaml +++ b/src/methods/batchelor_mnn_correct/config.vsh.yaml @@ -5,9 +5,9 @@ summary: Mutual nearest neighbors correction description: | Correct for batch effects in single-cell expression data using the mutual nearest neighbors method. references: - # Haghverdi, L., Lun, A., Morgan, M. et al. - # Batch effects in single-cell RNA-sequencing data are - # corrected by matching mutual nearest neighbors. + # Haghverdi, L., Lun, A., Morgan, M. et al. + # Batch effects in single-cell RNA-sequencing data are + # corrected by matching mutual nearest neighbors. # Nat Biotechnol 36, 421–427 (2018). https://doi.org/10.1038/nbt.4091 doi: 10.1038/nbt.4091 links: @@ -30,4 +30,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowcpu, highmem, midtime] + label: [lowcpu, highmem, hightime] diff --git a/src/methods/bbknn/config.vsh.yaml b/src/methods/bbknn/config.vsh.yaml index 7db6742c..6853d3df 100644 --- a/src/methods/bbknn/config.vsh.yaml +++ b/src/methods/bbknn/config.vsh.yaml @@ -48,4 +48,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, lowcpu] + label: [hightime, midmem, lowcpu] diff --git a/src/methods/combat/config.vsh.yaml b/src/methods/combat/config.vsh.yaml index 00d659f3..123e0fd9 100644 --- a/src/methods/combat/config.vsh.yaml +++ b/src/methods/combat/config.vsh.yaml @@ -33,4 +33,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, highmem, lowcpu] + label: [hightime, highmem, lowcpu] diff --git a/src/methods/geneformer/config.vsh.yaml b/src/methods/geneformer/config.vsh.yaml index 9624fa07..6be7998c 100644 --- a/src/methods/geneformer/config.vsh.yaml +++ b/src/methods/geneformer/config.vsh.yaml @@ -56,4 +56,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, midcpu, gpu] + label: [hightime, midmem, midcpu, gpu] diff --git a/src/methods/harmony/config.vsh.yaml b/src/methods/harmony/config.vsh.yaml index c94bc253..796edbcf 100644 --- a/src/methods/harmony/config.vsh.yaml +++ b/src/methods/harmony/config.vsh.yaml @@ -3,7 +3,7 @@ name: harmony label: Harmony summary: Fast, sensitive and accurate integration of single-cell data with Harmony description: | - Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. + Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. references: # Korsunsky, I., Millard, N., Fan, J. et al. @@ -30,4 +30,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowcpu, highmem, midtime] + label: [lowcpu, highmem, hightime] diff --git a/src/methods/harmonypy/config.vsh.yaml b/src/methods/harmonypy/config.vsh.yaml index 511229dd..37c99b2d 100644 --- a/src/methods/harmonypy/config.vsh.yaml +++ b/src/methods/harmonypy/config.vsh.yaml @@ -3,7 +3,7 @@ name: harmonypy label: Harmonypy summary: harmonypy is a port of the harmony R package by Ilya Korsunsky. description: | - Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. + Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. references: # Korsunsky, I., Millard, N., Fan, J. et al. @@ -31,4 +31,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowcpu, highmem, midtime] + label: [lowcpu, highmem, hightime] diff --git a/src/methods/liger/config.vsh.yaml b/src/methods/liger/config.vsh.yaml index ada022b2..b57e07f1 100644 --- a/src/methods/liger/config.vsh.yaml +++ b/src/methods/liger/config.vsh.yaml @@ -3,9 +3,9 @@ name: liger label: LIGER summary: Linked Inference of Genomic Experimental Relationships description: | - LIGER or linked inference of genomic experimental relationships uses iNMF - deriving and implementing a novel coordinate descent algorithm to efficiently - do the factorization. Joint clustering is performed and factor loadings are + LIGER or linked inference of genomic experimental relationships uses iNMF + deriving and implementing a novel coordinate descent algorithm to efficiently + do the factorization. Joint clustering is performed and factor loadings are normalised. references: doi: 10.1016/j.cell.2019.05.006 @@ -31,4 +31,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowcpu, highmem, midtime] + label: [lowcpu, highmem, hightime] diff --git a/src/methods/mnnpy/config.vsh.yaml b/src/methods/mnnpy/config.vsh.yaml index fb108de1..433b5780 100644 --- a/src/methods/mnnpy/config.vsh.yaml +++ b/src/methods/mnnpy/config.vsh.yaml @@ -57,4 +57,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, lowcpu, highmem] + label: [hightime, lowcpu, highmem] diff --git a/src/methods/pyliger/config.vsh.yaml b/src/methods/pyliger/config.vsh.yaml index 4ac31f39..9c0e9a4c 100644 --- a/src/methods/pyliger/config.vsh.yaml +++ b/src/methods/pyliger/config.vsh.yaml @@ -4,9 +4,9 @@ label: pyliger summary: Python implementation of LIGER (Linked Inference of Genomic Experimental Relationships description: | - LIGER (installed as rliger) is a package for integrating and analyzing multiple - single-cell datasets, developed by the Macosko lab and maintained/extended by the - Welch lab. It relies on integrative non-negative matrix factorization to identify + LIGER (installed as rliger) is a package for integrating and analyzing multiple + single-cell datasets, developed by the Macosko lab and maintained/extended by the + Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. references: doi: 10.1016/j.cell.2019.05.006 @@ -37,4 +37,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowcpu, highmem, midtime] + label: [lowcpu, highmem, hightime] diff --git a/src/methods/scalex/config.vsh.yaml b/src/methods/scalex/config.vsh.yaml index 2f4687e3..b42923ef 100644 --- a/src/methods/scalex/config.vsh.yaml +++ b/src/methods/scalex/config.vsh.yaml @@ -34,4 +34,4 @@ runners: - type: executable - type: nextflow directives: - label: [lowmem, lowcpu, midtime] + label: [lowmem, lowcpu, hightime] diff --git a/src/methods/scanorama/config.vsh.yaml b/src/methods/scanorama/config.vsh.yaml index d3e6b133..2bc43738 100644 --- a/src/methods/scanorama/config.vsh.yaml +++ b/src/methods/scanorama/config.vsh.yaml @@ -34,4 +34,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, highmem, lowcpu] + label: [hightime, highmem, lowcpu] diff --git a/src/methods/scanvi/config.vsh.yaml b/src/methods/scanvi/config.vsh.yaml index 5222fa16..17d69243 100644 --- a/src/methods/scanvi/config.vsh.yaml +++ b/src/methods/scanvi/config.vsh.yaml @@ -54,4 +54,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, lowmem, lowcpu, gpu] + label: [hightime, lowmem, lowcpu, gpu] diff --git a/src/methods/scgpt_zeroshot/config.vsh.yaml b/src/methods/scgpt_zeroshot/config.vsh.yaml index 23ea5931..858e2fe0 100644 --- a/src/methods/scgpt_zeroshot/config.vsh.yaml +++ b/src/methods/scgpt_zeroshot/config.vsh.yaml @@ -65,4 +65,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, midcpu, gpu] + label: [hightime, midmem, midcpu, gpu] diff --git a/src/methods/scimilarity/config.vsh.yaml b/src/methods/scimilarity/config.vsh.yaml index e2f29613..dc479b80 100644 --- a/src/methods/scimilarity/config.vsh.yaml +++ b/src/methods/scimilarity/config.vsh.yaml @@ -32,4 +32,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, lowcpu] + label: [hightime, midmem, lowcpu] diff --git a/src/methods/scprint/config.vsh.yaml b/src/methods/scprint/config.vsh.yaml index 5e57819c..b3ce9d4b 100644 --- a/src/methods/scprint/config.vsh.yaml +++ b/src/methods/scprint/config.vsh.yaml @@ -79,4 +79,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, midcpu, gpu] + label: [hightime, midmem, midcpu, gpu] diff --git a/src/methods/scvi/config.vsh.yaml b/src/methods/scvi/config.vsh.yaml index 9158759f..d1b0cfba 100644 --- a/src/methods/scvi/config.vsh.yaml +++ b/src/methods/scvi/config.vsh.yaml @@ -50,4 +50,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, lowcpu, gpu] + label: [hightime, midmem, lowcpu, gpu] diff --git a/src/methods/uce/config.vsh.yaml b/src/methods/uce/config.vsh.yaml index bd54a6d8..c67ea904 100644 --- a/src/methods/uce/config.vsh.yaml +++ b/src/methods/uce/config.vsh.yaml @@ -43,4 +43,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, highmem, midcpu, gpu] + label: [hightime, highmem, midcpu, gpu]