From 56fe1c1def6728576056d703cfb6ec58dbd73e3d Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Wed, 20 Jan 2021 23:22:26 +0100
Subject: [PATCH] [MODIF] fix bugs
---
main.nf | 22 +++++++++++-----------
nextflow.config | 7 +++++--
2 files changed, 16 insertions(+), 13 deletions(-)
diff --git a/main.nf b/main.nf
index f966e6a..4a79d99 100644
--- a/main.nf
+++ b/main.nf
@@ -274,7 +274,7 @@ if (params.res_dist_decay){
// Resolutions for contact maps
map_res = Channel.from( params.bin_size ).splitCsv().flatten()
-map_res.concat(comp_bin, tads_bin, ddecay_bin)
+map_res.concat(tads_bin, ddecay_bin)
.unique()
.set { map_res }
@@ -831,9 +831,8 @@ process build_contact_maps{
file chrsize from chromosome_size.collect()
output:
- file("*.matrix") into raw_maps, raw_maps_4cool
- file "*.bed"
-
+ set val(sample), val(mres), file("*.matrix"), file("*.bed") into raw_maps, raw_maps_4cool
+
script:
"""
build_matrix --matrix-format upper --binsize ${mres} --chrsizes ${chrsize} --ifile ${vpairs} --oprefix ${sample}_${mres}
@@ -853,11 +852,11 @@ process run_ice{
!params.skip_maps && !params.skip_ice
input:
- file(rmaps) from raw_maps
- file "*.biases"
+ set val(sample), val(res), file(rmaps), file(bed) from raw_maps
output:
- file("*iced.matrix") into iced_maps_4h5, iced_maps_4cool
+ set val(sample), val(res), file("*iced.matrix"), file(bed) into iced_maps_4h5, iced_maps_4cool
+ file ("*.biases") into iced_bias
script:
prefix = rmaps.toString() - ~/(\.matrix)?$/
@@ -884,10 +883,10 @@ process convert_to_cool {
input:
set val(sample), val(res), file(mat), file(bed) from iced_maps_4cool
- file chrsize from chrsize_cool.collect()
+ file chrsize from chromosome_size_cool.collect()
output:
- set val(sample), val(res), file("*cool") into cool_maps
+ set val(sample), val(res), file("*.cool") into cool_maps
file("*.mcool") into mcools_maps
script:
@@ -993,6 +992,7 @@ process tads_hicexplorer {
chIS = cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
+/*
process tads_insulation {
tag "$sample - $res"
label 'process_medium'
@@ -1012,7 +1012,7 @@ process tads_insulation {
cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv
"""
}
-
+*/
/*
@@ -1131,7 +1131,7 @@ workflow.onComplete {
def email_html = html_template.toString()
// Render the sendmail template
- def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
+ def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
def sf = new File("$projectDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
diff --git a/nextflow.config b/nextflow.config
index f184e67..71acfa7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -66,13 +66,16 @@ params {
ice_eps = 0.1
// Downstream Analysis
- res_dist_decay = 1000000
- res_tads = 40000,20000
+ res_dist_decay = '1000000'
+ tads_caller = "hicexplorer,insulation"
+ res_tads = '40000,20000'
// Workflow
skip_maps = false
skip_ice = false
skip_cool = false
+ skip_dist_decay = false
+ skip_tads = false
skip_multiqc = false
// Boilerplate options
--
GitLab