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nextflow.config
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nextflow.config
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manifest {
name = 'vib-singlecell-nf/vsn-pipelines'
description = 'A repository of pipelines for single-cell data in Nextflow DSL2'
homePage = 'https://github.com/vib-singlecell-nf/vsn-pipelines'
version = '0.25.0'
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=20.10.0'
}
// load these configs first:
includeConfig 'conf/global.config'
includeConfig 'conf/compute_resources.config'
includeConfig 'conf/test_disabled.config'
includeConfig 'src/utils/utils.config' // utilities config
profiles {
standard {
process.executor = 'local'
}
qsub {
process.executor = 'pbs'
}
docker {
includeConfig 'conf/docker.config'
}
singularity {
includeConfig 'conf/singularity.config'
}
vpcx {
includeConfig 'conf/vpcx.config'
}
min {
includeConfig 'conf/min.config'
}
test {
includeConfig 'conf/test.config'
}
// workflow-specific profiles:
star {
includeConfig 'src/star/star.config'
}
bbknn {
if(min && min.enabled) {
includeConfig 'src/scanpy/conf/min.config'
includeConfig 'src/scanpy/conf/bbknn.config'
} else {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scanpy/conf/bbknn.config'
}
includeConfig 'src/utils/conf/scope.config'
}
mnncorrect {
if(min && min.enabled) {
includeConfig 'src/scanpy/conf/min.config'
includeConfig 'src/scanpy/conf/mnncorrect.config'
} else {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scanpy/conf/mnncorrect.config'
}
includeConfig 'src/utils/conf/scope.config'
}
popscle {
includeConfig 'src/popscle/popscle.config'
}
harmony {
if(min && min.enabled) {
includeConfig 'src/scanpy/conf/min.config'
includeConfig 'src/harmony/harmony.config'
} else {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/harmony/harmony.config'
}
includeConfig 'src/utils/conf/scope.config'
}
harmony_only {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/harmony/harmony.config'
includeConfig 'src/utils/conf/scope.config'
}
bbknn_scenic {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scanpy/conf/bbknn.config'
includeConfig 'src/scenic/scenic.config'
includeConfig 'src/utils/conf/scope.config'
}
bbknn_scenic_multiruns {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scanpy/conf/bbknn.config'
includeConfig 'src/scenic/scenic.config'
includeConfig 'src/scenic/conf/multi_runs.config'
includeConfig 'src/utils/conf/scope.config'
}
single_sample {
if(min && min.enabled) {
includeConfig 'src/scanpy/conf/min.config'
} else {
includeConfig 'src/scanpy/scanpy.config'
}
includeConfig 'src/utils/conf/scope.config'
}
multi_sample {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/utils/conf/scope.config'
}
single_sample_scenic {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scenic/scenic.config'
includeConfig 'src/utils/conf/scope.config'
}
single_sample_scrublet {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scrublet/scrublet.config'
includeConfig 'src/utils/conf/scope.config'
}
single_sample_decontx_correct {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/utils/conf/scope.config'
includeConfig 'src/celda/celda.config'
includeConfig 'src/celda/conf/decontx_correct.config'
}
single_sample_decontx_filter_scrublet {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scrublet/scrublet.config'
includeConfig 'src/utils/conf/scope.config'
includeConfig 'src/celda/celda.config'
includeConfig 'src/celda/conf/decontx_filter.config'
}
single_sample_decontx_correct_scrublet {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scrublet/scrublet.config'
includeConfig 'src/utils/conf/scope.config'
includeConfig 'src/celda/celda.config'
includeConfig 'src/celda/conf/decontx_correct.config'
}
single_sample_soupx_correct_scrublet {
includeConfig 'src/scanpy/scanpy.config'
includeConfig 'src/scrublet/scrublet.config'
includeConfig 'src/utils/conf/scope.config'
includeConfig 'src/soupx/soupx.config'
includeConfig 'src/soupx/conf/soupx_correct.config'
}
scenic {
includeConfig 'src/scenic/scenic.config'
includeConfig 'src/utils/conf/scope.config'
}
scenic_append_only {
includeConfig 'src/scenic/conf/append.config'
}
scenic_multiruns {
includeConfig 'src/scenic/scenic.config'
includeConfig 'src/scenic/conf/multi_runs.config'
includeConfig 'src/utils/conf/scope.config'
}
single_sample_star {
includeConfig 'src/star/star.config'
includeConfig 'src/scanpy/scanpy.config'
}
nemesh {
includeConfig 'conf/nemesh.config'
includeConfig 'src/fastp/fastp.config'
includeConfig 'src/picard/picard.config'
includeConfig 'src/dropseqtools/dropseqtools.config'
includeConfig 'src/star/star.config'
includeConfig 'src/dropletutils/dropletutils.config'
}
// scanpy profiles:
scanpy_filter {
includeConfig 'src/scanpy/conf/scanpy_filter.config'
}
scanpy_data_transformation {
includeConfig 'src/scanpy/conf/data_transformation.config'
}
scanpy_normalization {
includeConfig 'src/scanpy/conf/normalization.config'
}
scanpy_regress_out {
includeConfig 'src/scanpy/conf/regress_out.config'
}
// cellranger profiles:
cellranger {
includeConfig 'src/cellranger/cellranger.config'
}
cellranger_libraries {
includeConfig 'src/cellranger/cellranger.config'
includeConfig 'src/cellranger/conf/cellranger_libraries.config'
}
cellranger_count {
includeConfig 'src/cellranger/conf/base.config'
includeConfig 'src/cellranger/conf/count.config'
}
cellranger_count_libraries {
includeConfig 'src/cellranger/conf/base.config'
includeConfig 'src/cellranger/conf/count.config'
includeConfig 'src/cellranger/conf/count_libraries.config'
}
cellranger_count_metadata {
includeConfig 'src/cellranger/conf/base.config'
includeConfig 'src/cellranger/conf/count.config'
includeConfig 'src/cellranger/conf/count_metadata.config'
}
// scrublet profiles
scrublet {
includeConfig 'src/scrublet/scrublet.config'
}
// celda profiles:
decontx {
includeConfig 'src/celda/celda.config'
includeConfig 'src/celda/conf/decontx_filter.config'
}
// soupx profiles
soupx {
includeConfig 'src/soupx/soupx.config'
includeConfig 'src/soupx/conf/soupx_correct.config'
}
// directs profiles:
directs {
includeConfig 'src/directs/directs.config'
}
// scope profiles:
scope {
includeConfig 'src/utils/conf/scope.config'
}
// data profiles:
tenx {
includeConfig 'src/channels/conf/tenx_cellranger_mex.config'
}
tenx_atac {
includeConfig 'src/channels/conf/tenx_atac_cellranger_mex.config'
}
tenx_h5 {
includeConfig 'src/channels/conf/tenx_cellranger_h5.config'
}
h5ad {
includeConfig 'src/channels/conf/h5ad.config'
}
loom {
includeConfig 'src/channels/conf/loom.config'
}
tsv {
includeConfig 'src/channels/conf/tsv.config'
}
csv {
includeConfig 'src/channels/conf/csv.config'
}
sra {
includeConfig 'src/channels/conf/sra.config'
includeConfig 'src/utils/conf/sra_metadata.config'
includeConfig 'src/sratoolkit/sratoolkit.config'
}
seurat_rds {
includeConfig 'src/channels/conf/seurat_rds.config'
}
fragments {
includeConfig 'src/channels/conf/fragments.config'
}
bam {
includeConfig 'src/channels/conf/bam.config'
}
// metadata profiles:
dm6 {
includeConfig 'src/scenic/conf/min/tfs/fly-v0.0.1.config'
includeConfig 'conf/genomes/dm6.config'
}
hg38 {
includeConfig 'src/scenic/conf/min/tfs/human-v0.0.1.config'
includeConfig 'conf/genomes/hg38.config'
}
hg19 {
includeConfig 'src/scenic/conf/min/tfs/human-v0.0.1.config'
includeConfig 'conf/genomes/hg19.config'
}
mm10 {
includeConfig 'src/scenic/conf/min/tfs/mouse-v0.0.1.config'
includeConfig 'conf/genomes/mm10.config'
}
// feature profiles:
pcacv {
includeConfig 'src/pcacv/pcacv.config'
}
// scenic profiles:
scenic_use_cistarget_motifs {
includeConfig "src/scenic/conf/min/dbs/cistarget-motifs-${params.global.species}-${params.global.genome.assembly}-v0.0.1.config"
}
scenic_use_cistarget_tracks {
includeConfig "src/scenic/conf/min/dbs/cistarget-tracks-${params.global.species}-${params.global.genome.assembly}-v0.0.1.config"
}
scenic_test {
includeConfig 'src/scenic/conf/test.config'
}
// utility profiles:
cell_filter_annotate_and_sample_annotate {
includeConfig 'src/utils/conf/cell_filter.config'
includeConfig 'src/utils/conf/cell_annotate.config'
includeConfig 'src/utils/conf/sample_annotate.config'
includeConfig 'src/utils/conf/h5ad_clean.config'
}
utils_sample_annotate {
includeConfig 'src/utils/conf/sample_annotate.config'
}
utils_cell_annotate {
includeConfig 'src/utils/conf/cell_annotate.config'
}
utils_cell_filter {
includeConfig 'src/utils/conf/cell_filter.config'
}
// cluster submission retry profile:
cluster_retry {
includeConfig 'conf/compute_resources_with_retry.config'
}
// logger profiles
log {
includeConfig 'conf/logger.config'
}
// test profiles:
test__single_sample {
includeConfig 'conf/test__single_sample.config'
}
test__single_sample_scenic {
includeConfig 'conf/genomes/hg38.config'
includeConfig 'conf/test__single_sample_scenic.config'
}
test__single_sample_scrublet {
includeConfig 'conf/test__single_sample_scrublet.config'
}
test__single_sample_param_exploration {
includeConfig 'conf/test__single_sample_param_exploration.config'
}
test__scenic {
includeConfig 'conf/genomes/hg38.config'
includeConfig 'conf/test__scenic.config'
}
test__scenic_multiruns {
includeConfig 'conf/genomes/hg38.config'
includeConfig 'conf/test__scenic_multiruns.config'
}
test__single_sample_scenic_multiruns {
includeConfig 'conf/genomes/hg38.config'
includeConfig 'conf/test__single_sample_scenic_multiruns.config'
}
test__bbknn {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'conf/test__bbknn.config'
}
test__bbknn_scenic {
includeConfig 'conf/genomes/hg38.config'
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'conf/test__bbknn_scenic.config'
}
test__harmony {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'conf/test__harmony.config'
}
test__mnncorrect {
includeConfig 'src/utils/conf/h5ad_concatenate.config'
includeConfig 'conf/test__mnncorrect.config'
}
test__decontx {
includeConfig 'conf/test__decontx.config'
}
test__single_sample_decontx_correct {
includeConfig 'conf/test__single_sample.config'
includeConfig 'conf/test__single_sample_decontx_correct.config'
}
test__single_sample_decontx_correct_scrublet {
includeConfig 'conf/test__single_sample_scrublet.config'
includeConfig 'conf/test__single_sample_decontx_correct_scrublet.config'
}
/*
*** ATAC-seq profiles ***
*/
cellranger_atac {
includeConfig 'src/cellranger-atac/cellranger-atac.config'
}
cellranger_atac_count {
includeConfig 'src/cellranger-atac/conf/base.config'
includeConfig 'src/cellranger-atac/conf/count.config'
}
cellranger_atac_count_metadata {
includeConfig 'src/cellranger-atac/conf/base.config'
includeConfig 'src/cellranger-atac/conf/count.config'
includeConfig 'src/cellranger-atac/conf/count_metadata.config'
}
cistopic {
includeConfig 'src/cistopic/cistopic.config'
}
atac_preprocess {
includeConfig 'conf/atac/preprocess.config'
}
atac_qc_filtering {
includeConfig 'conf/atac/qc_filtering.config'
}
atac_preprocess_freemuxlet {
includeConfig 'conf/atac/preprocess.config'
includeConfig 'src/popscle/popscle.config'
}
/*
*** the following profiles should be loaded last ***
*/
test__compute_resources {
// must be used with GitHub Actions tests to limit compute resources
includeConfig 'conf/test__compute_resources.config'
}
}
timeline {
enabled = true
file = "${params.global.outdir}/nextflow_reports/execution_timeline.html"
}
report {
enabled = true
file = "${params.global.outdir}/nextflow_reports/execution_report.html"
}
trace {
enabled = true
file = "${params.global.outdir}/nextflow_reports/execution_trace.txt"
}
dag {
enabled = true
file = "${params.global.outdir}/nextflow_reports/pipeline_dag.svg"
}
min {
enabled = false
}