Skip to content
Snippets Groups Projects
Commit 56fe1c1d authored by nservant's avatar nservant
Browse files

[MODIF] fix bugs

parent e51d04fe
No related branches found
No related tags found
No related merge requests found
...@@ -274,7 +274,7 @@ if (params.res_dist_decay){ ...@@ -274,7 +274,7 @@ if (params.res_dist_decay){
// Resolutions for contact maps // Resolutions for contact maps
map_res = Channel.from( params.bin_size ).splitCsv().flatten() 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() .unique()
.set { map_res } .set { map_res }
...@@ -831,9 +831,8 @@ process build_contact_maps{ ...@@ -831,9 +831,8 @@ process build_contact_maps{
file chrsize from chromosome_size.collect() file chrsize from chromosome_size.collect()
output: output:
file("*.matrix") into raw_maps, raw_maps_4cool set val(sample), val(mres), file("*.matrix"), file("*.bed") into raw_maps, raw_maps_4cool
file "*.bed"
script: script:
""" """
build_matrix --matrix-format upper --binsize ${mres} --chrsizes ${chrsize} --ifile ${vpairs} --oprefix ${sample}_${mres} build_matrix --matrix-format upper --binsize ${mres} --chrsizes ${chrsize} --ifile ${vpairs} --oprefix ${sample}_${mres}
...@@ -853,11 +852,11 @@ process run_ice{ ...@@ -853,11 +852,11 @@ process run_ice{
!params.skip_maps && !params.skip_ice !params.skip_maps && !params.skip_ice
input: input:
file(rmaps) from raw_maps set val(sample), val(res), file(rmaps), file(bed) from raw_maps
file "*.biases"
output: 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: script:
prefix = rmaps.toString() - ~/(\.matrix)?$/ prefix = rmaps.toString() - ~/(\.matrix)?$/
...@@ -884,10 +883,10 @@ process convert_to_cool { ...@@ -884,10 +883,10 @@ process convert_to_cool {
input: input:
set val(sample), val(res), file(mat), file(bed) from iced_maps_4cool 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: 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 file("*.mcool") into mcools_maps
script: script:
...@@ -993,6 +992,7 @@ process tads_hicexplorer { ...@@ -993,6 +992,7 @@ process tads_hicexplorer {
chIS = cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins") chIS = cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
/*
process tads_insulation { process tads_insulation {
tag "$sample - $res" tag "$sample - $res"
label 'process_medium' label 'process_medium'
...@@ -1012,7 +1012,7 @@ process tads_insulation { ...@@ -1012,7 +1012,7 @@ process tads_insulation {
cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv
""" """
} }
*/
/* /*
...@@ -1131,7 +1131,7 @@ workflow.onComplete { ...@@ -1131,7 +1131,7 @@ workflow.onComplete {
def email_html = html_template.toString() def email_html = html_template.toString()
// Render the sendmail template // Render the sendmail template
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$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 sf = new File("$projectDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString() def sendmail_html = sendmail_template.toString()
......
...@@ -66,13 +66,16 @@ params { ...@@ -66,13 +66,16 @@ params {
ice_eps = 0.1 ice_eps = 0.1
// Downstream Analysis // Downstream Analysis
res_dist_decay = 1000000 res_dist_decay = '1000000'
res_tads = 40000,20000 tads_caller = "hicexplorer,insulation"
res_tads = '40000,20000'
// Workflow // Workflow
skip_maps = false skip_maps = false
skip_ice = false skip_ice = false
skip_cool = false skip_cool = false
skip_dist_decay = false
skip_tads = false
skip_multiqc = false skip_multiqc = false
// Boilerplate options // Boilerplate options
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment