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Commit eb464357 authored by John Lafin's avatar John Lafin
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Fix sample sheet split

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with 15 additions and 9 deletions
workflow/main.nf
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...@@ -187,15 +187,21 @@ process setup { ...@@ -187,15 +187,21 @@ process setup {
workflow { workflow {
// Parse sample sheet // Parse sample sheet
sample_sheet = file(params.sample_sheet) sample_sheet = file(params.sample_sheet)
cr_input = channel.fromPath(params.sample_sheet) \ Channel
| splitCsv(header: true) \ .fromPath(params.sample_sheet)
| map{ row -> tuple( row.sample, row.cr_reference, row.cr_expect _cells, row.cr_chemistry, row.cr_introns, row.cr_create_bam ) } .splitCsv(header: true)
cb_input = channel.fromPath(params.sample_sheet) \ .map{ row -> tuple( row.sample, row.cr_reference, row.cr_expect_cells, row.cr_chemistry, row.cr_introns, row.cr_create_bam ) }
| splitCsv(header: true) \ .set { cr_input }
| map{ row -> tuple( row.sample, row.cb_expected_cells, row.cb_total_droplets_included, row.cb_fpr ) } Channel
qc_input = channel.fromPath(params.sample_sheet) \ .fromPath(params.sample_sheet)
| splitCsv(header: true) \ .splitCsv(header: true)
| map{ row -> tuple( row.sample, row.qc_nCount_threshold_lo, row.qc_nCount_threshold_hi, row.qc_nFeature_threshold_lo, row.qc_nFeature_threshold_hi, row.qc_percent.mito_threshold ) } .map{ row -> tuple( row.sample, row.cb_expected_cells, row.cb_total_droplets_included, row.cb_fpr ) }
.set { cb_input }
Channel
.fromPath(params.sample_sheet)
.splitCsv(header: true)
.map{ row -> tuple( row.sample, row.qc_nCount_threshold_lo, row.qc_nCount_threshold_hi, row.qc_nFeature_threshold_lo, row.qc_nFeature_threshold_hi, row.qc_percent_mito_threshold ) }
.set{ qc_input }
// Run cellranger count // Run cellranger count
fastq = channel.fromPath(params.fastq).collect() fastq = channel.fromPath(params.fastq).collect()
......
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