From 18dd092af7305d7a9b30962f620a46d028e803ab Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 28 Apr 2021 09:33:52 +0200
Subject: [PATCH] flexi_splitter: add main.nf and yaml example
---
src/nf_modules/flexi_splitter/main.nf | 43 +++++++++++++++++++
.../flexi_splitter/marseq_flexi_splitter.yaml | 41 ++++++++++++++++++
2 files changed, 84 insertions(+)
create mode 100644 src/nf_modules/flexi_splitter/main.nf
create mode 100644 src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
new file mode 100644
index 00000000..fdb5f29b
--- /dev/null
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -0,0 +1,43 @@
+version = "1.0.2"
+container_url = "lbmc/flexi_splitter:${version}"
+
+params.split = ""
+params.split_out = ""
+
+process split {
+ // You can get an example of config file here:
+ // src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_prefix"
+ if (params.split_out != "") {
+ publishDir "results/${params.split_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(reads)
+ tuple val(config_id), path(config)
+
+ output:
+ tuple val(file_id), path("*.fastq*"), emit: fastq
+
+ script:
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ } else {
+ file_prefix = file_id
+ }
+ def whitelist_param = ""
+ if (whitelist_id != "NO CONFIG"){
+ whitelist_param = "-w ${white_list}"
+ }
+
+ if (reads.size() == 2)
+ """
+ flexi_splitter ${params.split} -f ${reads[0]} ${read[1]} -c ${config} -o split
+ """
+ else
+ """
+ flexi_splitter ${params.split} -f ${reads[0]} -c ${config} -o split
+ """
+}
diff --git a/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml b/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
new file mode 100644
index 00000000..72f46d2d
--- /dev/null
+++ b/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
@@ -0,0 +1,41 @@
+PLATE:
+ coords:
+ reads: 0
+ start: 1
+ stop: 4
+ header: False
+ samples:
+ - name : Plate1
+ seq: GACT
+ - name : Plate2
+ seq: CATG
+ - name : Plate3
+ seq: CCAA
+ - name : Plate4
+ seq: CTGT
+ - name : Plate5
+ seq: GTAG
+ - name : Plate6
+ seq: TGAT
+ - name : Plate7
+ seq: ATCA
+ - name : Plate8
+ seq: TAGA
+
+conditions:
+ - Plate1 :
+ Plate1
+ - Plate2 :
+ Plate2
+ - Plate3 :
+ Plate3
+ - Plate4 :
+ Plate4
+ - Plate5 :
+ Plate5
+ - Plate6 :
+ Plate6
+ - Plate7 :
+ Plate7
+ - Plate8 :
+ Plate8
--
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