From a8ea256ad584c4460192c9d092ebbf6f5eec6560 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Tue, 9 Apr 2019 16:26:31 +0200
Subject: [PATCH] update CHANGELOG
---
CHANGELOG.md | 15 +++++++++++++--
main.nf | 23 ++++++-----------------
2 files changed, 19 insertions(+), 19 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0b88e32..2539792 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,15 @@
# nf-core/hic: Changelog
-## v1.0dev - <date>
-Initial release of nf-core/hic, created with the [nf-core](http://nf-co.re/) template.
+## v1.0dev - 2019-04-09
+
+ First version of nf-core-hic pipeline which is a Nextflow implementation of the HiC-Pro pipeline [https://github.com/nservant/HiC-Pro].
+ Note that all HiC-Pro functionalities are not yet all implemented. The current version is designed for protocols based on restriction enzyme digestion.
+
+ In summary, this version allows :
+ * Automatic detection and generation of annotation files based on igenomes if not provided.
+ * Two-steps alignment of raw sequencing reads
+ * Reads filtering and detection of valid interaction products
+ * Generation of raw contact matrices for a set of resolutions
+ * Normalization of the contact maps using the ICE algorithm
+ * Generation of cooler file for visualization on higlass [https://higlass.io/]
+ * Quality report based on HiC-Pro MultiQC module
diff --git a/main.nf b/main.nf
index 24783e2..53798f4 100644
--- a/main.nf
+++ b/main.nf
@@ -10,14 +10,6 @@
*/
-/*TOOO
-- outputs
-- multiqc
-- update version tools
-- install + compile
-*/
-
-
def helpMessage() {
log.info"""
=======================================================
@@ -75,6 +67,7 @@ def helpMessage() {
--ice_eps Convergence criteria for ICE normalization
Other options:
+ --splitFastq Size of read chuncks to use to speed up the workflow
--outdir The output directory where the results will be saved
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
@@ -101,14 +94,10 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
}
// Reference index path configuration
-// Define these here - after the profiles are loaded with the iGenomes paths
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
-//params.chromosome_size = false
-//params.restriction_fragments = false
-
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
custom_runName = params.name
@@ -203,7 +192,7 @@ else {
if ( params.chromosome_size ){
Channel.fromPath( params.chromosome_size , checkIfExists: true)
- .set {chromosome_size}
+ .into {chromosome_size; chromosome_size_cool}
}
else if ( params.fasta ){
Channel.fromPath( params.fasta )
@@ -356,7 +345,7 @@ if(!params.chromosome_size && params.fasta){
file fasta from fasta_for_chromsize
output:
- file "*.size" into chromosome_size
+ file "*.size" into chromosome_size, chromosome_size_cool
script:
"""
@@ -680,14 +669,14 @@ process run_ice{
/*
* STEP 5 - COOLER FILE
-
+ */
process generate_cool{
tag "$sample"
publishDir "${params.outdir}/export/cool", mode: 'copy'
input:
set val(sample), file(vpairs) from all_valid_pairs_4cool
- val chrsize from chromosome_size
+ file chrsize from chromosome_size_cool.collect()
output:
file("*mcool") into cool_maps
@@ -697,7 +686,7 @@ process generate_cool{
hicpro2higlass.sh -i $vpairs -r 5000 -c ${chrsize} -n
"""
}
-*/
+
/*
* STEP 5 - MultiQC
--
GitLab