/
cross_species_integration_multiple_species.nf
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cross_species_integration_multiple_species.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// © EMBL-European Bioinformatics Institute, 2023
// Updated upon containerization of BENGAL envs
// Yuyao Song <ysong@ebi.ac.uk>
// Oct 2023
log.info """
===========================================================
Cross-species integration and assessment - nextflow pipeline
- Integrate scRNA-seq data from multiple species - this workflow
- SCCAF projection on integrated data to assess integration quality
- harmony, scanorama, scVI - python based
- Seurat CCA, Seurat RPCA, fastMNN, LIGER, LIGER-UINMF - r based
Author: ysong@ebi.ac.uk
Mar 2022
===========================================================
"""
.stripIndent()
process harmony_integration {
label 'scanpy_based'
label 'regular_intg_resource'
publishDir "${params.results}/results/harmony/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_harmony_integrated.h5ad", emit: harmony_cross_species_h5ad_ch
path "${baseName}_harmony_integrated_UMAP.png", emit: harmony_cross_species_umap_ch
script:
"""
python ${projectDir}/bin/harmony_integration.py \
--batch_key ${params.batch_key} --species_key ${params.species_key} --cluster_key ${params.cluster_key} \
${file} ${baseName}_harmony_integrated.h5ad ${baseName}_harmony_integrated_UMAP.png
"""
}
process scanorama_integration {
label 'scanpy_based'
label 'regular_intg_resource'
publishDir "${params.results}/results/scanorama/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_scanorama_integrated.h5ad", emit: scanorama_cross_species_h5ad_ch
path "${baseName}_scanorama_integrated_UMAP.png", emit: scanorama_cross_species_umap_ch
script:
"""
python ${projectDir}/bin/scanorama_integration.py \
--batch_key ${params.batch_key} --species_key ${params.species_key} --cluster_key ${params.cluster_key} \
${file} ${baseName}_scanorama_integrated.h5ad ${baseName}_scanorama_integrated_UMAP.png
"""
}
// scVI uses GPU
process scvi_integration {
label 'scvi_based'
label 'GPU_intg_resource'
publishDir "${params.results}/results/scVI/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_scVI_integrated.h5ad", emit: scvi_cross_species_h5ad_ch
path "${baseName}_scVI_integrated_UMAP.png", emit: scvi_cross_species_umap_ch
script:
"""
python ${projectDir}/bin/scvi_integration.py \
--batch_key ${params.batch_key} --species_key ${params.species_key} --cluster_key ${params.cluster_key} \
${file} ${baseName}_scVI_integrated.h5ad ${baseName}_scVI_integrated_UMAP.png
"""
}
// scANVI uses GPU
process scanvi_integration {
label 'scvi_based'
label 'GPU_intg_resource'
publishDir "${params.results}/results/scANVI/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_scANVI_integrated.h5ad", emit: scanvi_cross_species_h5ad_ch
path "${baseName}_scANVI_integrated_UMAP.png", emit: scanvi_cross_species_umap_ch
script:
"""
python ${projectDir}/bin/scANVI_integration.py \
--batch_key ${params.batch_key} --species_key ${params.species_key} --cluster_key ${params.cluster_key} \
${file} ${baseName}_scANVI_integrated.h5ad ${baseName}_scANVI_integrated_UMAP.png ${baseName}_scANVI_integrated_mde.png
"""
}
process seurat_CCA_integration{
label 'seurat_based'
label 'bigmem_intg_resource'
publishDir "${params.results}/results/seuratCCA/cross_species/integrated_h5ad/", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_seuratCCA_integrated.rds", emit: seuratCCA_cross_species_rds_ch
path "${baseName}_seuratCCA_integrated_UMAP.pdf" , emit: seuratCCA_cross_species_umap_ch
script:
"""
Rscript ${projectDir}/bin/seurat_CCA_integration.R -i ${file} -o ${baseName}_seuratCCA_integrated.rds -p ${baseName}_seuratCCA_integrated_UMAP.pdf -b ${params.batch_key} -s ${params.species_key} -c ${params.cluster_key}
"""
}
process seurat_RPCA_integration{
label 'seurat_based'
label 'bigmem_intg_resource'
publishDir "${params.results}/results/seuratRPCA/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_seuratRPCA_integrated.rds" , emit: seuratRPCA_cross_species_rds_ch
path "${baseName}_seuratRPCA_integrated_UMAP.pdf" , emit: seuratRPCA_cross_species_umap_ch
script:
"""
Rscript ${projectDir}/bin/seurat_RPCA_integration.R -i ${file} -o ${baseName}_seuratRPCA_integrated.rds -p ${baseName}_seuratRPCA_integrated_UMAP.pdf -b ${params.batch_key} -s ${params.species_key} -c ${params.cluster_key}
"""
}
process fastMNN_integration{
label 'R_based'
label 'regular_intg_resource'
publishDir "${params.results}/results/fastMNN/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_fastMNN_integrated.rds" , emit: fastMNN_cross_species_rds_ch
path "${baseName}_fastMNN_integrated_UMAP.pdf" , emit: fastMNN_cross_species_UMAP_ch
script:
"""
Rscript ${projectDir}/bin/fastMNN_integration.R -i ${file} -o ${baseName}_fastMNN_integrated.rds -p ${baseName}_fastMNN_integrated_UMAP.pdf -b ${params.batch_key} -s ${params.species_key} -c ${params.cluster_key}
"""
}
process liger_integration{
label 'R_based'
label 'regular_intg_resource'
publishDir "${params.results}/results/LIGER/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(file)
output:
path "${baseName}_LIGER_integrated.rds", emit: liger_cross_species_rds_ch
path "${baseName}_LIGER_integrated_UMAP.pdf", emit: liger_cross_species_UMAP_ch
script:
"""
Rscript ${projectDir}/bin/LIGER_integration.R -i ${file} -o ${baseName}_LIGER_integrated.rds -p ${baseName}_LIGER_integrated_UMAP.pdf -b ${params.batch_key} -s ${params.species_key} -c ${params.cluster_key}
"""
}
process rligerUINMF_integration{
label 'R_based'
label 'regular_intg_resource'
publishDir "${params.results}/results/rligerUINMF/cross_species/integrated_h5ad", mode: 'copy'
input:
tuple val(baseName), path(metadata)
output:
path "*_rligerUINMF_integrated.rds"
path "*_rligerUINMF_integrated_UMAP.pdf"
script:
"""
mkdir -p ${params.results}/results/rligerUINMF/cross_species/integrated_h5ad && \
Rscript ${projectDir}/bin/rliger_integration_UINMF_multiple_species.R \
--basename ${baseName} \
--metadata ${params.liger_metadata} \
--out_dir . \
--cluster_key ${params.cluster_key}
"""
}
// nextflow will search for the output file in the cwd
// so set the out_dir in the script to cwd, then nextflow will copy the results to the publishDir anyway
workflow {
all_homology_h5ad_mapped_ch = Channel.fromPath(params.homology_concat_h5ad)
.map { file -> tuple(file.baseName, file) }
all_homology_rds_mapped_ch = Channel.fromPath(params.homology_concat_rds)
.map { file -> tuple(file.baseName, file) }
concatenated_h5ad = all_homology_h5ad_mapped_ch
concatenated_h5ad.view()
harmony_integration(concatenated_h5ad)
scanorama_integration(concatenated_h5ad)
scvi_integration(concatenated_h5ad)
scanvi_integration(concatenated_h5ad)
concatenated_rds = all_homology_rds_mapped_ch
seurat_CCA_integration(concatenated_rds)
seurat_RPCA_integration(concatenated_rds)
fastMNN_integration(concatenated_rds)
liger_integration(concatenated_rds)
liger_metadata = Channel.fromPath(params.liger_metadata)
.map { file -> tuple(file.baseName, file) }
liger_metadata.view()
rligerUINMF_integration(liger_metadata)
}