From dbe9d6798ac61d456c4fec31aa4e9a7efe9e090f Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Mon, 11 Oct 2021 11:39:13 +0200
Subject: [PATCH] yaml modification
---
src/chipster.nf | 2 +-
src/config.yml | 23 ++++++++++++++++++++++-
2 files changed, 23 insertions(+), 2 deletions(-)
diff --git a/src/chipster.nf b/src/chipster.nf
index 525d66a8..d753bffb 100755
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -51,7 +51,7 @@ params.project = ""
/* Params from config file yaml: */
-data = params.config.collect {k , v -> "${params.fastq_folder}/${v.fastq.gz}"}
+data = params.input.collect {k , v -> "${params.fastq}/${v.fastq.gz}"}
/* Params out */
params.fastp_out = "$params.project/fastp/"
diff --git a/src/config.yml b/src/config.yml
index 1b3b999e..2135abcd 100644
--- a/src/config.yml
+++ b/src/config.yml
@@ -1,8 +1,24 @@
input:
+ # A row defines some features to describe a sample to analyse.
+ # You can add as many row as you want below each other. Be sure that
+ # the name of the row is the same as the file name witout extension.
+
+ # project name,
+
+ # boolean value to setup sequencing type (paired-end or single-end)
+ paired-end: FALSE
+
+ # directory containing fastq files (rawdata)
+ fastq_folder: ""
+
row1:
- sample: 5Y_siDDX_CTCF
+ # sample must be a string. It corresponds to the name of the sample
+ sample: "5Y_siDDX_CTCF"
+ # fastq is the corresponding fastq file, can be compressed as gz file.
fastq: "5Y_siDDX_CTCF.fastq.gz"
+ # condition
condition: "siDDX"
+ # type is related to ChIP type: Input or IP
type: "IP"
row2:
@@ -10,3 +26,8 @@ input:
fastq: "5Y_siDDX_input.fastq.gz"
condition: "siDDX"
type: "Input"
+
+
+ # Under construction:
+ # Organism (hg19, GRCH38, HBV...) default hg19 for FasterDB compatibility
+ # organism: ""
\ No newline at end of file
--
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