From 462bb713dc7a04f68617beda01fc1f6e79f23834 Mon Sep 17 00:00:00 2001
From: user name <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Wed, 10 Aug 2022 17:05:51 +0100
Subject: [PATCH] Alternative samplesheet for cnv calling - bam/bai files
instead of fastq1/fastq2
---
pipeline/inputs.nf | 22 +++++++++++++++-------
1 file changed, 15 insertions(+), 7 deletions(-)
diff --git a/pipeline/inputs.nf b/pipeline/inputs.nf
index d73f38a..de6222f 100644
--- a/pipeline/inputs.nf
+++ b/pipeline/inputs.nf
@@ -39,7 +39,7 @@ workflow read_inputs {
/*
- ch_samplesheet_info - Tuple channel of individual ID, r1 fastqs and r2 fastqs:
+ ch_samplesheet_info - Tuple channel of individual ID, r1 fastqs and r2 fastqs -OR- BAM and BAI files:
[
[
indv1,
@@ -53,11 +53,19 @@ workflow read_inputs {
]
*/
ch_samplesheet = Channel.fromPath(params.sample_sheet, checkIfExists: true)
- ch_samplesheet_info = ch_samplesheet.splitCsv(sep:'\t', header: true)
- .map(
- { line -> [line.individual_id, file(line.read_1), file(line.read_2), line.bam]}
- )
- .groupTuple()
+
+ if (params.workflow == 'variant-calling') {
+ ch_samplesheet_info = ch_samplesheet.splitCsv(sep:'\t', header: true)
+ .map(
+ { line -> [line.individual_id, file(line.read_1), file(line.read_2)]}
+ )
+ .groupTuple()
+ } else if (params.workflow == 'cnv-calling') {
+ ch_samplesheet_info = ch_samplesheet.splitCsv(sep:'\t', header: true)
+ .map(
+ { line -> [line.individual_id, file(line.bam), file(line.bai)]}
+ )
+ }
/*
ch_individuals - merge of samplesheet and ped file information:
@@ -97,7 +105,7 @@ workflow read_inputs {
]
*/
ch_individuals_by_family = ch_individuals.map({[it[1], it]})
-
+
emit:
ch_ped_file = ch_ped_file
ch_ped_file_info = ch_ped_file_info
--
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