Commit e27e275a authored by Xavier Grand's avatar Xavier Grand
Browse files

fonctionnel SE

parent c6497eb4
......@@ -42,10 +42,21 @@ if (params.paired_end) {
error "Not Implemented"
/*
Channel
.fromFilePairs( params.input.collect { k, v -> "${params.fastq_folder}/${v{1,2}.fastq}", size: 2 )
.fromPath( params.input.collect { k, v -> "${params.fastq_folder}/${v.fastq1}" })
.ifEmpty { error "No fastq file defined" }
.set { fastq_files }
*/
.set { fastq1 }
Channel
.fromPath( params.input.collect { k, v -> "${params.fastq_folder}/${v.fastq2}" })
.ifEmpty { error "No fastq file defined" }
.set { fastq2 }
fastq_files =
fastq1
.concat(fastq2)
.groupBy()
*/
} else {
Channel
......
nextflow.enable.dsl=2
// "${params.fastq_folder}/*R{1,2}.fastq.gz} with fromFilePairs
Channel
.fromPath( "/media/adminxavier/Expansion/HBV/202112_CutnTag_GG/rawdata/gui2/10_S10_L001_R1.fastq.gz" )
.ifEmpty { error "Cannot find fastq R1 file." }
.set { fastq1 }
Channel
.fromPath( "/media/adminxavier/Expansion/HBV/202112_CutnTag_GG/rawdata/gui2/10_S10_L001_R2.fastq.gz" )
.ifEmpty { error "Cannot find fastq R2 file." }
.set { fastq2 }
fastq_files = fastq1
.concat(fastq2)
.groupBy
/*
idx_genome = "${params.idx}*.bt2"
Channel
......@@ -10,6 +27,8 @@ Channel
genome_indexed_input.view()
/*
/* Channel
.from([[1, "fastq1.fq"], [2, "fastq2.fq"], [3, "fastq3.fq"], [4, "fastq4.fq"]])
.set{ fastq_files }
......
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