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main_atac.nf
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import static groovy.json.JsonOutput.*
nextflow.enable.dsl=2
include {
INIT;
} from './src/utils/workflows/utils' params(params)
INIT(params)
include {
SC__FILE_CONVERTER;
} from './src/utils/processes/utils' params(params)
include {
getDataChannel;
} from './src/channels/channels' params(params)
/*
ATAC-seq pipelines
*/
// runs mkfastq, then cellranger-atac count:
workflow cellranger_atac {
include {
CELLRANGER_ATAC
} from './src/cellranger-atac/main.nf' params(params)
CELLRANGER_ATAC(
file(params.sc.cellranger_atac.mkfastq.csv),
file(params.sc.cellranger_atac.mkfastq.runFolder),
file(params.sc.cellranger_atac.count.reference)
)
}
workflow cistopic {
include {
cistopic as CISTOPIC
} from './src/cistopic/main' params(params)
getDataChannel | CISTOPIC
}
workflow atac_preprocess {
// generic ATAC-seq preprocessing pipeline: adapter trimming, mapping, fragments file generation
include {
ATAC_PREPROCESS_WITH_METADATA;
} from './workflows/atac/preprocess.nf' params(params)
ATAC_PREPROCESS_WITH_METADATA(file(params.data.atac_preprocess.metadata))
}
workflow atac_preprocess_bap {
include {
ATAC_PREPROCESS_WITH_METADATA;
} from './workflows/atac/preprocess.nf' params(params)
include {
get_bam;
BAP__BARCODE_MULTIPLET_PIPELINE;
} from './src/bap/main.nf' params(params)
ATAC_PREPROCESS_WITH_METADATA(file(params.data.atac_preprocess.metadata)) |
get_bam |
BAP__BARCODE_MULTIPLET_PIPELINE
}
workflow bap {
include {
BAP__BARCODE_MULTIPLET_PIPELINE;
} from './src/bap/main.nf' params(params)
getDataChannel | BAP__BARCODE_MULTIPLET_PIPELINE
}
/*
QC
*/
workflow atac_qc_filtering {
include {
ATAC_QC_PREFILTER;
} from './workflows/atac/qc_filtering.nf' params(params)
getDataChannel | ATAC_QC_PREFILTER
}
workflow atac_preprocess_freemuxlet {
// generic ATAC-seq preprocessing pipeline: adapter trimming, mapping, fragments file generation
include {
ATAC_PREPROCESS_WITH_METADATA;
} from './workflows/atac/preprocess.nf' params(params)
include {
freemuxlet as FREEMUXLET;
} from './workflows/popscle' params(params)
ATAC_PREPROCESS_WITH_METADATA(file(params.sc.atac.preprocess.metadata))
FREEMUXLET(ATAC_PREPROCESS_WITH_METADATA.out.bam)
}