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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,98 +1,98 @@ | ||
| #!/usr/bin/env nextflow | ||
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| // | ||
| // Demultiplex Element Biosciences bases data using bases2fastq | ||
| // | ||
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| include { MGIKIT_DEMULTIPLEX as DEMULTIPLEX } from "../../../modules/nf-core/mgikit/demultiplex/main" | ||
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| workflow MGIKIT_DEMULTIPLEX { | ||
| take: | ||
| ch_flowcell // [[id:"", lane:""],samplesheet.csv, path/to/bases/files] | ||
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| main: | ||
| DEMULTIPLEX( ch_flowcell ) | ||
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| // Generate meta for each fastq | ||
| ch_fastq_with_meta = generate_fastq_meta(DEMULTIPLEX.out.fastq) | ||
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| emit: | ||
| fastq = ch_fastq_with_meta | ||
| unassigned = DEMULTIPLEX.out.undetermined | ||
| ambiguous = DEMULTIPLEX.out.ambiguous | ||
| qc_reports = DEMULTIPLEX.out.qc_reports; | ||
| versions = DEMULTIPLEX.out.versions | ||
| } | ||
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||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| FUNCTIONS | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
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| // Add meta values to fastq channel | ||
| def generate_fastq_meta(ch_reads) { | ||
| // Create a tuple with the meta.id and the fastq | ||
| ch_reads.transpose().map{ | ||
| fc_meta, fastq -> | ||
| def meta = [ | ||
| "id": fastq.getSimpleName().toString().replaceAll(/_S\d+_L0\d+_R\d+.*$/, ""), | ||
| "samplename": fastq.getSimpleName().toString() - ~/_S\d+_L0\d+_R\d+.*$/, | ||
| "readgroup": [:], | ||
| "fcid": fc_meta.id, | ||
| "lane": fc_meta.lane | ||
| ] | ||
| meta.readgroup = readgroup_from_fastq(fastq) | ||
| meta.readgroup.SM = meta.samplename | ||
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| return [ meta , fastq ] | ||
| } | ||
| // Group by meta.id for PE samples | ||
| .groupTuple(by: [0]) | ||
| // Add meta.single_end | ||
| .map { | ||
| meta, fastq -> | ||
| if (fastq.size() == 1){ | ||
| meta.single_end = true | ||
| } else { | ||
| meta.single_end = false | ||
| } | ||
| return [ meta, fastq.flatten() ] | ||
| } | ||
| } | ||
|
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||
| // https://github.com/nf-core/sarek/blob/7ba61bde8e4f3b1932118993c766ed33b5da465e/workflows/sarek.nf#L1014-L1040 | ||
| def readgroup_from_fastq(path) { | ||
| // expected format: | ||
| // xx:yy:FLOWCELLID:LANE:... (seven fields) | ||
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| def line | ||
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| path.withInputStream { | ||
| InputStream gzipStream = new java.util.zip.GZIPInputStream(it) | ||
| Reader decoder = new InputStreamReader(gzipStream, 'ASCII') | ||
| BufferedReader buffered = new BufferedReader(decoder) | ||
| line = buffered.readLine() | ||
| } | ||
| assert line.startsWith('@') | ||
| line = line.substring(1) | ||
| def fields = line.split(':') | ||
| //println(line); | ||
| //println(fields); | ||
| def rg = [:] | ||
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| // https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq | ||
| // "@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos>:UMI <read>:N:0:<index sequence>" | ||
| sequencer_serial = fields[0] | ||
| run_nubmer = fields[1] | ||
| fcid = fields[2] | ||
| lane = fields[3] | ||
| index = fields[-1] =~ /[GATC+-]/ ? fields[-1] : "" | ||
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| rg.ID = [fcid,lane].join(".") | ||
| rg.PU = [fcid, lane, index].findAll().join(".") | ||
| // TODO: @edmundmiller verify if this is correct | ||
| rg.PL = "ELEMENT" | ||
|
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| return rg | ||
| } | ||
| #!/usr/bin/env nextflow | ||
|
|
||
| // | ||
| // Demultiplex Element Biosciences bases data using bases2fastq | ||
| // | ||
|
|
||
| include { MGIKIT_DEMULTIPLEX as DEMULTIPLEX } from "../../../modules/nf-core/mgikit/demultiplex/main" | ||
|
|
||
| workflow MGIKIT_DEMULTIPLEX { | ||
| take: | ||
| ch_flowcell // [[id:"", lane:""],samplesheet.csv, path/to/bases/files] | ||
|
|
||
| main: | ||
| DEMULTIPLEX( ch_flowcell ) | ||
|
|
||
| // Generate meta for each fastq | ||
| ch_fastq_with_meta = generate_fastq_meta(DEMULTIPLEX.out.fastq) | ||
|
|
||
| emit: | ||
| fastq = ch_fastq_with_meta | ||
| unassigned = DEMULTIPLEX.out.undetermined | ||
| ambiguous = DEMULTIPLEX.out.ambiguous | ||
| qc_reports = DEMULTIPLEX.out.qc_reports; | ||
| versions = DEMULTIPLEX.out.versions | ||
| } | ||
|
|
||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| FUNCTIONS | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
|
|
||
| // Add meta values to fastq channel | ||
| def generate_fastq_meta(ch_reads) { | ||
| // Create a tuple with the meta.id and the fastq | ||
| ch_reads.transpose().map{ | ||
| fc_meta, fastq -> | ||
| def meta = [ | ||
| "id": fastq.getSimpleName().toString().replaceAll(/_S\d+_L0\d+_R\d+.*$/, ""), | ||
| "samplename": fastq.getSimpleName().toString() - ~/_S\d+_L0\d+_R\d+.*$/, | ||
| "readgroup": [:], | ||
| "fcid": fc_meta.id, | ||
| "lane": fc_meta.lane | ||
| ] | ||
| meta.readgroup = readgroup_from_fastq(fastq) | ||
| meta.readgroup.SM = meta.samplename | ||
|
|
||
| return [ meta , fastq ] | ||
| } | ||
| // Group by meta.id for PE samples | ||
| .groupTuple(by: [0]) | ||
| // Add meta.single_end | ||
| .map { | ||
| meta, fastq -> | ||
| if (fastq.size() == 1){ | ||
| meta.single_end = true | ||
| } else { | ||
| meta.single_end = false | ||
| } | ||
| return [ meta, fastq.flatten() ] | ||
| } | ||
| } | ||
|
|
||
| // https://github.com/nf-core/sarek/blob/7ba61bde8e4f3b1932118993c766ed33b5da465e/workflows/sarek.nf#L1014-L1040 | ||
| def readgroup_from_fastq(path) { | ||
| // expected format: | ||
| // xx:yy:FLOWCELLID:LANE:... (seven fields) | ||
|
|
||
| def line | ||
|
|
||
| path.withInputStream { | ||
| InputStream gzipStream = new java.util.zip.GZIPInputStream(it) | ||
| Reader decoder = new InputStreamReader(gzipStream, 'ASCII') | ||
| BufferedReader buffered = new BufferedReader(decoder) | ||
| line = buffered.readLine() | ||
| } | ||
| assert line.startsWith('@') | ||
| line = line.substring(1) | ||
| def fields = line.split(':') | ||
| //println(line); | ||
| //println(fields); | ||
| def rg = [:] | ||
|
|
||
| // https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq | ||
| // "@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos>:UMI <read>:N:0:<index sequence>" | ||
| sequencer_serial = fields[0] | ||
| run_nubmer = fields[1] | ||
| fcid = fields[2] | ||
| lane = fields[3] | ||
| index = fields[-1] =~ /[GATC+-]/ ? fields[-1] : "" | ||
|
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||
| rg.ID = [fcid,lane].join(".") | ||
| rg.PU = [fcid, lane, index].findAll().join(".") | ||
| // TODO: @edmundmiller verify if this is correct | ||
| rg.PL = "ELEMENT" | ||
|
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| return rg | ||
| } |