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Commit a8ea256a authored by nservant's avatar nservant
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update CHANGELOG

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# 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
......@@ -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
......
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