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main.nf
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main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// import workflow of interest
if (params.workflow == "rnaseq"){
include {RNASEQ} from './workflows/rnaseq'
}
else if (params.workflow == "wes"){
include {WES} from './workflows/wes'
}
else if (params.workflow == "somatic_wes"){
include {SOMATIC_WES} from './workflows/somatic_wes'
}
else if (params.workflow == "somatic_wes_pta"){
include {SOMATIC_WES_PTA} from './workflows/somatic_wes_pta'
}
else if (params.workflow == "wgs"){
include {WGS} from './workflows/wgs'
}
else if (params.workflow == "rrbs"){
include {RRBS} from './workflows/rrbs'
}
else if (params.workflow == "atac"){
include {ATAC} from './workflows/atac'
}
else if (params.workflow == "chipseq"){
include {CHIPSEQ} from './workflows/chipseq'
}
else if (params.workflow == "pta"){
include {PTA} from './workflows/pta'
}
else if (params.workflow == "rna_fusion"){
include {RNA_FUSION} from './workflows/rna_fusion'
}
else if (params.workflow == "generate_pseudoreference"){
include {GENERATE_PSEUDOREFERENCE} from './workflows/generate_pseudoreference'
}
else if (params.workflow == "prepare_emase"){
include {PREPARE_EMASE} from './workflows/prepare_emase'
}
else if (params.workflow == "prep_do_gbrs_inputs"){
include {PREP_DO_GBRS_INPUT} from './subworkflows/prep_do_gbrs_inputs'
}
else if (params.workflow == "emase"){
include {EMASE} from './workflows/emase'
}
else if (params.workflow == "gbrs"){
include {GBRS} from './workflows/gbrs'
}
else if (params.workflow == "amplicon"){
include {AMPLICON} from './workflows/amplicon_fingerprint'
}
else if (params.workflow == "amplicon_generic"){
include {AMPLICON} from './workflows/amplicon_generic'
}
else if (params.workflow == "ancestry"){
include {ANCESTRY_RUN} from './workflows/ancestry'
}
else if (params.workflow == "germline_sv") {
// mmrsvd
include {GERMLINE_SV} from "./workflows/germline_sv"
}
else {
// if workflow name is not supported:
exit 1, "ERROR: No valid pipeline called. '--workflow ${params.workflow}' is not a valid workflow name."
}
// conditional to launch appropriate workflow
workflow{
if (params.workflow == "rnaseq"){
RNASEQ()
}
if (params.workflow == "wes"){
WES()
}
if (params.workflow == "somatic_wes"){
SOMATIC_WES()
}
if (params.workflow == "somatic_wes_pta"){
SOMATIC_WES_PTA()
}
if (params.workflow == "wgs"){
WGS()
}
if (params.workflow == "rrbs"){
RRBS()
}
if (params.workflow == "atac"){
ATAC()
}
if (params.workflow == "chipseq"){
CHIPSEQ()
}
if (params.workflow == "pta"){
PTA()
}
if (params.workflow == "rna_fusion"){
RNA_FUSION()
}
if (params.workflow == "generate_pseudoreference") {
GENERATE_PSEUDOREFERENCE()
}
if (params.workflow == "prepare_emase"){
PREPARE_EMASE()
}
if (params.workflow == "emase"){
EMASE()
}
if (params.workflow == "gbrs"){
GBRS()
}
if (params.workflow == "prep_do_gbrs_inputs"){
PREP_DO_GBRS_INPUT()
}
if (params.workflow == "amplicon" || params.workflow == "amplicon_generic"){
AMPLICON()
}
if (params.workflow == "ancestry"){
ANCESTRY_RUN()
}
if (params.workflow == "germline_sv") {
GERMLINE_SV()
}
}