From 2d3c99c639bd5cc8af1003b5bd474be0eeb00122 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 17:38:10 +0200
Subject: [PATCH] src/example_chipseq.nf: work in progress of chip-seq example
---
src/example_chipseq.nf | 123 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 123 insertions(+)
create mode 100644 src/example_chipseq.nf
diff --git a/src/example_chipseq.nf b/src/example_chipseq.nf
new file mode 100644
index 00000000..454617c9
--- /dev/null
+++ b/src/example_chipseq.nf
@@ -0,0 +1,123 @@
+
+nextflow.enable.dsl=2
+
+include {
+ fastp
+} from './nf_modules/fastp/main'
+
+workflow csv_parsing {
+ if (params.csv_path.size() > 0) {
+ log.info "loading local csv files"
+ Channel
+ .fromPath(params.csv_path, checkIfExists: true)
+ .ifEmpty { error
+ log.error """
+ =============================================================
+ WARNING! No csv input file precised.
+ Use '--csv_path <file.csv>'
+ Or '--help' for more informations
+ =============================================================
+ """
+ }
+ .splitCsv(header: true, sep: ";", strip: true)
+ .flatMap{
+ it -> [
+ [(it.IP + it.WCE).md5(), "IP", "w", file(it.IP)],
+ [(it.IP + it.WCE).md5(), "WCE", "w", file(it.WCE)]
+ ]
+ }
+ .map{ it ->
+ if (it[1] instanceof List){
+ it
+ } else {
+ [it[0], [it[1]], it[2], it[3], [it[4]]]
+ }
+ }
+ .map{
+ it ->
+ if (it[1].size() == 2){ // if data are paired_end
+ [
+ "index": it[0],
+ "group": ref_order(it),
+ "ip": it[2],
+ "type": it[3],
+ "id": read_order(it)[0],
+ "file": read_order(it)
+ ]
+ } else {
+ [
+ "index": it[0],
+ "group": it[1].simpleName,
+ "ip": it[2],
+ "type": it[3],
+ "id": it[4].simpleName,
+ "file": [it[4].simpleName, it[4]]
+ ]
+ }
+ }
+ .set{input_csv}
+ } else {
+ log.info "loading remotes SRA csv files"
+ Channel
+ .fromPath(params.csv_sra, checkIfExists: true)
+ .ifEmpty { error
+ log.error """
+ =============================================================
+ WARNING! No csv input file precised.
+ Use '--csv_path <file.csv>' or
+ Use '--csv_SRA <file.csv>'
+ Or '--help' for more informations
+ =============================================================
+ """
+ }
+ .splitCsv(header: true, sep: ";", strip: true)
+ .flatMap{
+ it -> [
+ [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], t.IP_w, "IP", "w", it.IP_w],
+ [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], it.IP_w, "WCE", "w", it.WCE_w],
+ [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], it.IP_w, "IP", "m", it.IP_m],
+ [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], it.IP_w, "WCE", "m", it.WCE_m]
+ ]
+ }
+ .map{
+ it ->
+ if (it[1].size() == 2){ // if data are paired_end
+ [
+ "index": (
+ it[0][0][0].simpleName +
+ it[0][0][1].simpleName +
+ it[0][0][2].simpleName +
+ it[0][0][3].simpleName
+ ).md5(),
+ "group": it[1][0].simpleName,
+ "ip": it[2],
+ "type": it[3],
+ "id": it[4][0].simpleName[0..-4],
+ "file": [it[4][0].simpleName[0..-4], it[4]]
+ ]
+ } else {
+ [
+ "index": (
+ it[0][0].simpleName +
+ it[0][1].simpleName +
+ it[0][2].simpleName +
+ it[0][3].simpleName
+ ).md5(),
+ "group": it[1].simpleName,
+ "ip": it[2],
+ "type": it[3],
+ "id": it[4].simpleName,
+ "file": [it[4].simpleName, it[4]]
+ ]
+ }
+ }
+ .set{input_csv}
+ }
+ emit:
+ input_csv
+}
+
+
+workflow {
+
+}
\ No newline at end of file
--
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