diff --git a/README.md b/README.md
index c49680ef112674b41b825b09e4112d1f1fab1dd3..90bf7b25b3feb388d37597a8f6602871fd4a3ca6 100644
--- a/README.md
+++ b/README.md
@@ -259,6 +259,12 @@ Gitlab developers
<br /><br />
## WHAT'S NEW IN
+### v1.10
+
+Parall debugged<br />
+Check in python part improved
+
+
### v1.9
Zipping added
diff --git a/bin/fisher_lod.py b/bin/fisher_lod.py
index 87cb4de927f849a0d91f970a5655dbfc2608e622..f4565189d5b36fbdcb570707786d0346c0b630c6 100644
--- a/bin/fisher_lod.py
+++ b/bin/fisher_lod.py
@@ -50,6 +50,7 @@ import pandas as pd
import numpy as np
import random # for shuffle() function
import warnings # for warnings.catch_warnings()
+from itertools import compress
################################ End Initialization
@@ -394,7 +395,7 @@ if all([i0 == 'NULL' for i0 in tsv_extra_fields]) is False:
tempo_pos.append(i2)
if all([i1 in vcf_csq_subfield_titles for i1 in csq_subfield_name]) is not True:
- sys.exit("\n\n========\n\nError in fisher_lod.py: some of the CSQ subfield of the tsv_extra_fields parameter (starting by CSQ_): \n"+" ".join(csq_subfield_name)+"\nare not in the vcf_csq_subfield_titles parameter: \n"+" ".join(vcf_csq_subfield_titles)+"\n\n========\n\n")
+ sys.exit("\n\n========\n\nError in fisher_lod.py: some of the CSQ subfield of the tsv_extra_fields parameter (starting by CSQ_): \n"+" ".join(csq_subfield_name)+"\nare not in the vcf_csq_subfield_titles parameter: \n"+" ".join(vcf_csq_subfield_titles)+"\nThe wrong fields are:\n"+" ".join(compress(vcf_csq_subfield_titles, [ not i1 in vcf_csq_subfield_titles for i1 in csq_subfield_name]))+"\n\n========\n\n")
else:
for i2 in csq_subfield_name:
for i3 in list(range(0, len(vcf_csq_subfield_titles))):
@@ -403,10 +404,10 @@ if all([i0 == 'NULL' for i0 in tsv_extra_fields]) is False:
tsv_extra_fields_wo_csq = [tsv_extra_fields[i1] for i1 in tempo_pos]
if all([i1 in vcf_info_field_titles for i1 in tsv_extra_fields_wo_csq]) is not True:
- sys.exit("\n\n========\n\nError in fisher_lod.py: not considering CSQ_, some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\n\n========\n\n")
+ sys.exit("\n\n========\n\nError in fisher_lod.py: not considering CSQ_, some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields_wo_csq)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\nThe wrong fields are:\n"+" ".join(compress(vcf_info_field_titles, [ not i1 in vcf_info_field_titles for i1 in tsv_extra_fields_wo_csq]))+"\n\n========\n\n")
elif all([i1 in vcf_info_field_titles for i1 in tsv_extra_fields]) is not True:
- sys.exit("\n\n========\n\nError in fisher_lod.py: some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\n\n========\n\n")
+ sys.exit("\n\n========\n\nError in fisher_lod.py: some of the tsv_extra_fields parameter values: \n"+" ".join(tsv_extra_fields)+"\nare not in the vcf_info_field_titles parameter: \n"+" ".join(vcf_info_field_titles)+"\nThe wrong fields are:\n"+" ".join(compress(vcf_info_field_titles, [ not i1 in vcf_info_field_titles for i1 in tsv_extra_fields]))+"\n\n========\n\n")
else:
tsv_extra_fields_wo_csq = tsv_extra_fields
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/trace.txt b/example of results/PL_family_WGS_fisher_1664887581/reports/trace.txt
deleted file mode 100644
index ac24540e7624ce578b62e1102d2d80b8b957761f..0000000000000000000000000000000000000000
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/trace.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
-2 a6/97eb2e 832 vcf_subfield_title (1) CACHED 0 2022-10-04 13:52:15.217 6.3s 4.6s 35.4% 104.1 MB 220.7 MB 12.1 MB 3.1 KB
-4 60/e7928c 1503 fisher (1) CACHED 0 2022-10-04 13:52:25.502 1m 54s 1m 53s 56.9% 182.6 MB 1.4 GB 16.6 MB 13.1 MB
-6 80/63f662 3791 tsv_compress (1) CACHED 0 2022-10-04 13:56:45.929 824ms 355ms 69.0% 4.6 MB 10 MB 13.2 MB 1.1 MB
-7 6f/0a9199 4203 miami_plot (1) CACHED 0 2022-10-04 13:56:49.959 4.4s 3.9s 60.1% 179.8 MB 319.3 MB 27.3 MB 83.6 KB
-3 72/140b27 5145 Backup COMPLETED 0 2022-10-04 14:46:23.921 691ms 7ms 24.0% 0 0 152 KB 335 B
-1 da/2bc735 5282 WorkflowVersion COMPLETED 0 2022-10-04 14:46:24.623 878ms 445ms 20.9% 3.4 MB 13.5 MB 185.7 KB 1.5 KB
-5 c6/848297 5485 tsv2vcf (1) COMPLETED 0 2022-10-04 14:46:25.511 3.2s 2.7s 34.8% 7.5 MB 17.9 MB 28.1 MB 14.6 MB
diff --git a/example of results/PL_family_WGS_fisher_1664887581/miami.png b/example of results/PL_family_WGS_fisher_1664893405/miami.png
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/miami.png
rename to example of results/PL_family_WGS_fisher_1664893405/miami.png
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/Log_info.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/Log_info.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/Log_info.txt
rename to example of results/PL_family_WGS_fisher_1664893405/reports/Log_info.txt
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/Run_info.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/Run_info.txt
similarity index 89%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/Run_info.txt
rename to example of results/PL_family_WGS_fisher_1664893405/reports/Run_info.txt
index 474e079ae859a3ebb9b7775f8d02bba757dd3ccf..6f34b716632c0eefc34aad906526c0cbd84a7f98 100644
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/Run_info.txt
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/Run_info.txt
@@ -1,9 +1,9 @@
Project (empty means no .git folder where the main.nf file is present): origin git@gitlab.pasteur.fr:gmillot/fisher_for_vcf.git (fetch)
-Git info (empty means no .git folder where the main.nf file is present): v1.8-dirty
-Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume
+Git info (empty means no .git folder where the main.nf file is present): v1.9-dirty
+Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config
execution mode: local
Manifest's pipeline version: null
-result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1664887581
+result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1664893405
nextflow version: 21.04.2
@@ -16,5 +16,5 @@ workDir (directory where tasks temporary files are created): /mnt/c/Users/Gael/D
USER VARIABLES:
-out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1664887581
+out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1664893405
sample_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/dag.dot b/example of results/PL_family_WGS_fisher_1664893405/reports/dag.dot
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/dag.dot
rename to example of results/PL_family_WGS_fisher_1664893405/reports/dag.dot
index 1e26b35f42e1dc9e74e5d62d390bdcf168631839..53fb309502e54ecef061cbc51f3bc29d41143cab 100644
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/dag.dot
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/dag.dot
@@ -55,10 +55,6 @@ p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p22 [label="tsv_compress"];
p11 -> p22 [label="fisher_ch5"];
-p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p21 [label="tsv2vcf"];
-p11 -> p21 [label="fisher_ch4"];
-
p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p12 [shape=point];
p11 -> p12 [label="fisher_ch2"];
@@ -67,6 +63,10 @@ p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
p20 [label="miami_plot"];
p11 -> p20 [label="fisher_ch3"];
+p11 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
+p21 [label="tsv2vcf"];
+p11 -> p21 [label="fisher_ch4"];
+
p13 [shape=point,label="",fixedsize=true,width=0.1];
p20 [label="miami_plot"];
p13 -> p20 [label="chr"];
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/fisher_for_vcf.config b/example of results/PL_family_WGS_fisher_1664893405/reports/fisher_for_vcf.config
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/fisher_for_vcf.config
rename to example of results/PL_family_WGS_fisher_1664893405/reports/fisher_for_vcf.config
index 303801668df4d417eac53c887cdb508a62caccee..d37a758775eb7c0417c09265359d82125d3ef7ec 100644
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/fisher_for_vcf.config
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/fisher_for_vcf.config
@@ -22,7 +22,7 @@ env {
chr_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
//chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
region = "none" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "none" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
- tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required
+ tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required. Warning: use a single space between strings
x_lim = "chr1" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
bottom_y_column = "NULL" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file. Then, explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
color_column = "AF" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/fisher_report.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/fisher_report.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/fisher_report.txt
rename to example of results/PL_family_WGS_fisher_1664893405/reports/fisher_report.txt
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/miami_report.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/miami_report.txt
similarity index 97%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/miami_report.txt
rename to example of results/PL_family_WGS_fisher_1664893405/reports/miami_report.txt
index 3a08934bd46ddd9687b5d49801bf11a3c4d14561..d1f87cc1c100b93b159dde9fb1b10e831cf8e392 100644
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/miami_report.txt
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/miami_report.txt
@@ -12,7 +12,7 @@
-2022-10-04 11:56:52
+2022-10-04 14:25:37
@@ -31,7 +31,7 @@
-END TIME: 2022-10-04 11:56:54
+END TIME: 2022-10-04 14:25:38
@@ -121,7 +121,7 @@ loaded via a namespace (and not attached):
################################ JOB END
-TIME: 2022-10-04 11:56:54
+TIME: 2022-10-04 14:25:38
TOTAL TIME LAPSE: 2S
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/report.html b/example of results/PL_family_WGS_fisher_1664893405/reports/report.html
similarity index 98%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/report.html
rename to example of results/PL_family_WGS_fisher_1664893405/reports/report.html
index 30b2c1bcbde484fabfd6b1421ae34a8f0458da3d..80858b276e1c3e1e9e8ee35d21129623af4d50f0 100644
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/report.html
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/report.html
@@ -18,11 +18,11 @@
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
- <meta name="description" content="Nextflow workflow report for run id [elegant_mercator]">
+ <meta name="description" content="Nextflow workflow report for run id [determined_mendel]">
<meta name="author" content="Paolo Di Tommaso, Phil Ewels">
<link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
- <title>[elegant_mercator] Nextflow Workflow Report</title>
+ <title>[determined_mendel] Nextflow Workflow Report</title>
<style type="text/css">
/*!
@@ -137,7 +137,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<li class="nav-item"><a class="nav-link" href="#tasks">Tasks</a></li>
</ul>
<span class="navbar-text">
- [elegant_mercator]
+ [determined_mendel]
</span>
</div>
</nav>
@@ -146,7 +146,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<div class="container">
<h1 class="display-3">Nextflow workflow report</h1>
- <h2 class="text-muted mb-4"><samp>[elegant_mercator]</samp> <em>(resumed run)</em></h2>
+ <h2 class="text-muted mb-4"><samp>[determined_mendel]</samp> </h2>
<div class="alert alert-success mb-4">
@@ -157,26 +157,26 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<dl>
<dt>Run times</dt>
<dd>
- <span id="workflow_start">04-Oct-2022 14:46:22</span> - <span id="workflow_complete">04-Oct-2022 14:46:28</span>
- (<span id="completed_fromnow"></span>duration: <strong>6.4s</strong>)
+ <span id="workflow_start">04-Oct-2022 16:23:26</span> - <span id="workflow_complete">04-Oct-2022 16:25:39</span>
+ (<span id="completed_fromnow"></span>duration: <strong>2m 13s</strong>)
</dd>
<dl>
<div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;">
- <div style="width: 42.86%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="3 tasks succeeded"><span class="text-truncate"> 3 succeeded </span></div>
- <div style="width: 57.14%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="4 tasks were cached"><span class="text-truncate"> 4 cached </span></div>
+ <div style="width: 100.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="7 tasks succeeded"><span class="text-truncate"> 7 succeeded </span></div>
+ <div style="width: 0.0%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="0 tasks were cached"><span class="text-truncate"> 0 cached </span></div>
<div style="width: 0.0%" class="progress-bar bg-warning" data-toggle="tooltip" data-placement="top" title="0 tasks reported and error and were ignored"><span class="text-truncate"> 0 ignored </span></div>
<div style="width: 0.0%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="0 tasks failed"><span class="text-truncate"> 0 failed </span></div>
</div>
</dl>
<dt>Nextflow command</dt>
- <dd><pre class="nfcommand"><code>nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume</code></pre></dd>
+ <dd><pre class="nfcommand"><code>nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config</code></pre></dd>
</dl>
<dl class="row small">
<dt class="col-sm-3">CPU-Hours</dt>
- <dd class="col-sm-9"><samp>0.5 (97.3% cached)</samp></dd>
+ <dd class="col-sm-9"><samp>0.5</samp></dd>
<dt class="col-sm-3">Launch directory</dt>
<dd class="col-sm-9"><samp>/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf</samp></dd>
@@ -194,11 +194,11 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<dt class="col-sm-3">Script ID</dt>
- <dd class="col-sm-9"><code>5c46e5da3bb23e8b4389b6cec3b4cdb9</code></dd>
+ <dd class="col-sm-9"><code>a2ab3fae17c5e4fd11e2b41b0356320c</code></dd>
<dt class="col-sm-3">Workflow session</dt>
- <dd class="col-sm-9"><code>64e6d84e-fcc9-4878-989d-bf1466e3b1fd</code></dd>
+ <dd class="col-sm-9"><code>c7bd182f-9655-4b2f-8617-ee50f6cb0c39</code></dd>
@@ -1029,7 +1029,7 @@ $(function() {
// Nextflow report data
window.data = { "trace":[
-{"task_id":"3","hash":"72\/140b27","native_id":"5145","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1664887583921","start":"1664887583948","complete":"1664887584612","duration":"691","realtime":"7","%cpu":"24.0","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"155605","wchar":"335","syscr":"252","syscw":"14","read_bytes":"521216","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/72\/140b27dcc31c757fcda1e1dc4c8ee9","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664887581\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"2","hash":"a6\/97eb2e","native_id":"832","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"CACHED","exit":"0","submit":"1664884335217","start":"1664884335302","complete":"1664884341502","duration":"6285","realtime":"4577","%cpu":"35.4","%mem":"0.1","rss":"109142016","vmem":"231399424","peak_rss":"109142016","peak_vmem":"231432192","rchar":"12700614","wchar":"3160","syscr":"1666","syscw":"243","read_bytes":"17606656","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/a6\/97eb2e56222f537f7976454a01a0ec","script":"\n #!\/bin\/bash -ue\n vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664884290\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"16306","inv_ctxt":"37"},{"task_id":"4","hash":"60\/e7928c","native_id":"1503","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"CACHED","exit":"0","submit":"1664884345502","start":"1664884345506","complete":"1664884459322","duration":"113820","realtime":"113379","%cpu":"56.9","%mem":"0.2","rss":"188891136","vmem":"1512030208","peak_rss":"191467520","peak_vmem":"1514741760","rchar":"17389402","wchar":"13700500","syscr":"2068","syscw":"1951","read_bytes":"53383168","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/60\/e7928c4db6f5aaab2b2e834362981f","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" \"vcf_csq_subfield_titles.txt\" \"fisher_report.txt\"\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664884290\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"610784","inv_ctxt":"1551"},{"task_id":"6","hash":"80\/63f662","native_id":"3791","process":"tsv_compress","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv_compress (1)","status":"CACHED","exit":"0","submit":"1664884605929","start":"1664884606021","complete":"1664884606753","duration":"824","realtime":"355","%cpu":"69.0","%mem":"0.0","rss":"4866048","vmem":"10412032","peak_rss":"4866048","peak_vmem":"10436608","rchar":"13859892","wchar":"1196538","syscr":"683","syscw":"17","read_bytes":"580608","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/80\/63f66252dfbc210d864f2b3eae209f","script":"\n #!\/bin\/bash -ue\n gzip -cf9 fisher.tsv > res.tsv.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664884602\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"95","inv_ctxt":"275"},{"task_id":"7","hash":"6f\/0a9199","native_id":"4203","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"CACHED","exit":"0","submit":"1664884609959","start":"1664884610051","complete":"1664884614392","duration":"4433","realtime":"3945","%cpu":"60.1","%mem":"0.2","rss":"188518400","vmem":"334737408","peak_rss":"188518400","peak_vmem":"334774272","rchar":"28603659","wchar":"85585","syscr":"5938","syscw":"225","read_bytes":"42279936","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/6f\/0a91997fdbe6b2bff501a0ae2438d5","script":"\n #!\/bin\/bash -ue\n miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1\" \"NULL\" \"AF\" \"3\" \"2\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664884602\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"5815","inv_ctxt":"14"},{"task_id":"1","hash":"da\/2bc735","native_id":"5282","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1664887584623","start":"1664887584712","complete":"1664887585501","duration":"878","realtime":"445","%cpu":"20.9","%mem":"0.0","rss":"3596288","vmem":"14155776","peak_rss":"3596288","peak_vmem":"14168064","rchar":"190186","wchar":"1514","syscr":"363","syscw":"35","read_bytes":"4763648","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/da\/2bc735070706c3460cae2c5da54a94","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664887581\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664887581\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664887581\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"17","inv_ctxt":"0"},{"task_id":"5","hash":"c6\/848297","native_id":"5485","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1664887585511","start":"1664887585601","complete":"1664887588721","duration":"3210","realtime":"2718","%cpu":"34.8","%mem":"0.0","rss":"7831552","vmem":"18702336","peak_rss":"7831552","peak_vmem":"18735104","rchar":"29503226","wchar":"15355176","syscr":"2676","syscw":"18454","read_bytes":"1340416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c6\/8482972734d06377b4a50c26e60770","script":"\n #!\/bin\/bash -ue\n PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n echo -e $PREHEADER > res.vcf\n FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\") # recover a file name without path\n FILE_EXTENSION=\"${FILENAME##*.}\" # ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz | awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' >> res.vcf\n else\n awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz >> res.vcf\n fi\n awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n NR==1{\n print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n print \"##INFO=<FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \">\\n\" ;\n print var1\"\\n\"\n }\n NR > 1{\n gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \"\\n\"\n }\n \' fisher.tsv >> res.vcf\n bgzip -f -l 9 res.vcf > res.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n tabix -p vcf res.vcf.gz # htslib command\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664887581\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"18933","inv_ctxt":"11"}], "summary":[{"cpuUsage":{"mean":35.4,"min":35.4,"q1":35.4,"q2":35.4,"q3":35.4,"max":35.4,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title 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+{"task_id":"3","hash":"0d\/5b51e8","native_id":"13763","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1664893407861","start":"1664893407876","complete":"1664893408442","duration":"581","realtime":"7","%cpu":"31.4","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"155642","wchar":"339","syscr":"252","syscw":"14","read_bytes":"521216","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/0d\/5b51e8e4a22b5e8ac8b81064c09383","script":"\n echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"1","hash":"93\/a34bfa","native_id":"13886","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1664893408465","start":"1664893408542","complete":"1664893409371","duration":"906","realtime":"385","%cpu":"18.7","%mem":"0.0","rss":"5124096","vmem":"14155776","peak_rss":"5124096","peak_vmem":"14168064","rchar":"190241","wchar":"1510","syscr":"365","syscw":"35","read_bytes":"3900416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/93\/a34bfa1a67e95b1cb2e2d2f7d7d16a","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config\" >> Run_info.txt\n echo \"execution mode\": local >> Run_info.txt\n modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n if [[ ! -z $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\" >> Run_info.txt\n echo \"nextflow version: 21.04.2\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT 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(1)","status":"COMPLETED","exit":"0","submit":"1664893409381","start":"1664893409471","complete":"1664893413021","duration":"3640","realtime":"3164","%cpu":"39.8","%mem":"0.1","rss":"108040192","vmem":"230297600","peak_rss":"108040192","peak_vmem":"230330368","rchar":"12700699","wchar":"3191","syscr":"1666","syscw":"243","read_bytes":"16881664","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/19\/6f56d4bf71a29ad670d835fd0667bc","script":"\n #!\/bin\/bash -ue\n vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz \"cute_little_R_functions.R\" \"vcf_subfield_title_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"9305","inv_ctxt":"7"},{"task_id":"4","hash":"ca\/cbdf86","native_id":"14402","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1664893413072","start":"1664893413121","complete":"1664893529642","duration":"116570","realtime":"116095","%cpu":"56.9","%mem":"0.2","rss":"189132800","vmem":"1512464384","peak_rss":"191479808","peak_vmem":"1514819584","rchar":"17390802","wchar":"13700504","syscr":"2069","syscw":"1951","read_bytes":"52962304","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/ca\/cbdf86a26ba5d10cff7014846b0d3f","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" \"vcf_csq_subfield_titles.txt\" \"fisher_report.txt\"\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"599486","inv_ctxt":"1698"},{"task_id":"5","hash":"4f\/a93d49","native_id":"16215","process":"tsv_compress","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv_compress (1)","status":"COMPLETED","exit":"0","submit":"1664893530189","start":"1664893530243","complete":"1664893531081","duration":"892","realtime":"356","%cpu":"69.1","%mem":"0.0","rss":"5312512","vmem":"10412032","peak_rss":"5312512","peak_vmem":"10436608","rchar":"13859941","wchar":"1196542","syscr":"683","syscw":"17","read_bytes":"580608","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/4f\/a93d49343ad2c2e80ff1bc6d16272f","script":"\n #!\/bin\/bash -ue\n gzip -cf9 fisher.tsv > res.tsv.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"110","inv_ctxt":"0"},{"task_id":"7","hash":"42\/37c3b8","native_id":"16363","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1664893531089","start":"1664893531181","complete":"1664893534471","duration":"3382","realtime":"2867","%cpu":"33.7","%mem":"0.0","rss":"7692288","vmem":"18702336","peak_rss":"7692288","peak_vmem":"18735104","rchar":"29503265","wchar":"15359277","syscr":"2676","syscw":"18454","read_bytes":"1340416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/42\/37c3b88bb11fd02d250c8e29c1718b","script":"\n #!\/bin\/bash -ue\n PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n echo -e $PREHEADER > res.vcf\n FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\") # recover a file name without path\n FILE_EXTENSION=\"${FILENAME##*.}\" # ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz | awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' >> res.vcf\n else\n awk \'{\n if($0 ~ \"^##.*\"){\n print $0\n }else{\n exit 0\n }\n }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz >> res.vcf\n fi\n awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n NR==1{\n print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n print \"##INFO=<FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \">\\n\" ;\n print var1\"\\n\"\n }\n NR > 1{\n gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n print \"\\n\"\n }\n \' fisher.tsv >> res.vcf\n bgzip -f -l 9 res.vcf > res.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n tabix -p vcf res.vcf.gz # htslib command\n ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"18176","inv_ctxt":"12"},{"task_id":"6","hash":"8d\/387f93","native_id":"16656","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"COMPLETED","exit":"0","submit":"1664893534480","start":"1664893534571","complete":"1664893539062","duration":"4582","realtime":"4129","%cpu":"58.8","%mem":"0.2","rss":"186990592","vmem":"334254080","peak_rss":"186990592","peak_vmem":"334286848","rchar":"28603706","wchar":"85589","syscr":"5938","syscw":"225","read_bytes":"42298368","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/8d\/387f93087f4062500842eebb2c1c3e","script":"\n #!\/bin\/bash -ue\n miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1\" \"NULL\" \"AF\" \"3\" \"2\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=NULL\ncolor_column=AF\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1664893405\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"5545","inv_ctxt":"13"}], 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</script>
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/timeline.html b/example of results/PL_family_WGS_fisher_1664893405/reports/timeline.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/timeline.html
rename to example of results/PL_family_WGS_fisher_1664893405/reports/timeline.html
index d931ed0ca790caf01cdcdc78c96795ff0bfb4d1a..f7f3df8a4ccc94e19a287d9ce65e9311d4385cc7 100644
--- a/example of results/PL_family_WGS_fisher_1664887581/reports/timeline.html
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/timeline.html
@@ -205,17 +205,17 @@ $(function() {
// Nextflow report data
window.data = {
- "elapsed": "6.8s",
- "beginningMillis": 1664884335217,
- "endingMillis": 1664887589281,
+ "elapsed": "2m 13s",
+ "beginningMillis": 1664893406431,
+ "endingMillis": 1664893539587,
"processes": [
- {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1664887583921, "ending_time": 1664887583948}, {"starting_time": 1664887583948, "ending_time": 1664887583955, "label": "691ms \/ 0"}, {"starting_time": 1664887583955, "ending_time": 1664887584612}]},
- {"label": "vcf_subfield_title (1)", "cached": true, "index": 1, "times": [{"starting_time": 1664884335217, "ending_time": 1664884335302}, {"starting_time": 1664884335302, "ending_time": 1664884339879, "label": "6.3s \/ 104.1 MB \/ CACHED"}, {"starting_time": 1664884339879, "ending_time": 1664884341502}]},
- {"label": "fisher (1)", "cached": true, "index": 2, "times": [{"starting_time": 1664884345502, "ending_time": 1664884345506}, {"starting_time": 1664884345506, "ending_time": 1664884458885, "label": "1m 54s \/ 182.6 MB \/ CACHED"}, {"starting_time": 1664884458885, "ending_time": 1664884459322}]},
- {"label": "tsv_compress (1)", "cached": true, "index": 3, "times": [{"starting_time": 1664884605929, "ending_time": 1664884606021}, {"starting_time": 1664884606021, "ending_time": 1664884606376, "label": "824ms \/ 4.6 MB \/ CACHED"}, {"starting_time": 1664884606376, "ending_time": 1664884606753}]},
- {"label": "miami_plot (1)", "cached": true, "index": 4, "times": [{"starting_time": 1664884609959, "ending_time": 1664884610051}, {"starting_time": 1664884610051, "ending_time": 1664884613996, "label": "4.4s \/ 179.8 MB \/ CACHED"}, {"starting_time": 1664884613996, "ending_time": 1664884614392}]},
- {"label": "WorkflowVersion", "cached": false, "index": 5, "times": [{"starting_time": 1664887584623, "ending_time": 1664887584712}, {"starting_time": 1664887584712, "ending_time": 1664887585157, "label": "878ms \/ 3.4 MB"}, {"starting_time": 1664887585157, "ending_time": 1664887585501}]},
- {"label": "tsv2vcf (1)", "cached": false, "index": 6, "times": [{"starting_time": 1664887585511, "ending_time": 1664887585601}, {"starting_time": 1664887585601, "ending_time": 1664887588319, "label": "3.2s \/ 7.5 MB"}, {"starting_time": 1664887588319, "ending_time": 1664887588721}]}
+ {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1664893407861, "ending_time": 1664893407876}, {"starting_time": 1664893407876, "ending_time": 1664893407883, "label": "581ms \/ 0"}, {"starting_time": 1664893407883, "ending_time": 1664893408442}]},
+ {"label": "WorkflowVersion", "cached": false, "index": 1, "times": [{"starting_time": 1664893408465, "ending_time": 1664893408542}, {"starting_time": 1664893408542, "ending_time": 1664893408927, "label": "906ms \/ 4.9 MB"}, {"starting_time": 1664893408927, "ending_time": 1664893409371}]},
+ {"label": "vcf_subfield_title (1)", "cached": false, "index": 2, "times": [{"starting_time": 1664893409381, "ending_time": 1664893409471}, {"starting_time": 1664893409471, "ending_time": 1664893412635, "label": "3.6s \/ 103 MB"}, {"starting_time": 1664893412635, "ending_time": 1664893413021}]},
+ {"label": "fisher (1)", "cached": false, "index": 3, "times": [{"starting_time": 1664893413072, "ending_time": 1664893413121}, {"starting_time": 1664893413121, "ending_time": 1664893529216, "label": "1m 57s \/ 182.6 MB"}, {"starting_time": 1664893529216, "ending_time": 1664893529642}]},
+ {"label": "tsv_compress (1)", "cached": false, "index": 4, "times": [{"starting_time": 1664893530189, "ending_time": 1664893530243}, {"starting_time": 1664893530243, "ending_time": 1664893530599, "label": "892ms \/ 5.1 MB"}, {"starting_time": 1664893530599, "ending_time": 1664893531081}]},
+ {"label": "tsv2vcf (1)", "cached": false, "index": 5, "times": [{"starting_time": 1664893531089, "ending_time": 1664893531181}, {"starting_time": 1664893531181, "ending_time": 1664893534048, "label": "3.4s \/ 7.3 MB"}, {"starting_time": 1664893534048, "ending_time": 1664893534471}]},
+ {"label": "miami_plot (1)", "cached": false, "index": 6, "times": [{"starting_time": 1664893534480, "ending_time": 1664893534571}, {"starting_time": 1664893534571, "ending_time": 1664893538700, "label": "4.6s \/ 178.3 MB"}, {"starting_time": 1664893538700, "ending_time": 1664893539062}]}
]
}
;
diff --git a/example of results/PL_family_WGS_fisher_1664893405/reports/trace.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/trace.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdd459f4549326a77a83bf13a48cddf7facc92bc
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/trace.txt
@@ -0,0 +1,8 @@
+task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
+3 0d/5b51e8 13763 Backup COMPLETED 0 2022-10-04 16:23:27.861 581ms 7ms 31.4% 0 0 152 KB 339 B
+1 93/a34bfa 13886 WorkflowVersion COMPLETED 0 2022-10-04 16:23:28.465 906ms 385ms 18.7% 4.9 MB 13.5 MB 185.8 KB 1.5 KB
+2 19/6f56d4 14095 vcf_subfield_title (1) COMPLETED 0 2022-10-04 16:23:29.381 3.6s 3.2s 39.8% 103 MB 219.7 MB 12.1 MB 3.1 KB
+4 ca/cbdf86 14402 fisher (1) COMPLETED 0 2022-10-04 16:23:33.072 1m 57s 1m 56s 56.9% 182.6 MB 1.4 GB 16.6 MB 13.1 MB
+5 4f/a93d49 16215 tsv_compress (1) COMPLETED 0 2022-10-04 16:25:30.189 892ms 356ms 69.1% 5.1 MB 10 MB 13.2 MB 1.1 MB
+7 42/37c3b8 16363 tsv2vcf (1) COMPLETED 0 2022-10-04 16:25:31.089 3.4s 2.9s 33.7% 7.3 MB 17.9 MB 28.1 MB 14.6 MB
+6 8d/387f93 16656 miami_plot (1) COMPLETED 0 2022-10-04 16:25:34.480 4.6s 4.1s 58.8% 178.3 MB 318.8 MB 27.3 MB 83.6 KB
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/vcf_csq_subfield_titles.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/vcf_csq_subfield_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/vcf_csq_subfield_titles.txt
rename to example of results/PL_family_WGS_fisher_1664893405/reports/vcf_csq_subfield_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1664887581/reports/vcf_info_field_titles.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/vcf_info_field_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/reports/vcf_info_field_titles.txt
rename to example of results/PL_family_WGS_fisher_1664893405/reports/vcf_info_field_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1664893405/reports/vcf_subfield_title_report.txt b/example of results/PL_family_WGS_fisher_1664893405/reports/vcf_subfield_title_report.txt
new file mode 100644
index 0000000000000000000000000000000000000000..682b006e1e091a0f49a6e3b955d1fc41e28fe5e4
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1664893405/reports/vcf_subfield_title_report.txt
@@ -0,0 +1,114 @@
+
+
+################################################################ vcf_subfield_title PROCESS
+
+
+
+
+
+
+################################ RUNNING DATE AND STARTING TIME
+
+
+
+
+2022-10-04 14:23:32
+
+
+
+
+
+
+################################ RUNNING
+
+
+
+
+
+
+################################ RUNNING END
+
+
+
+
+END TIME: 2022-10-04 14:23:32
+
+
+
+
+TOTAL TIME LAPSE: 0S
+
+
+
+
+ALL DATA SAVED IN all_objects.RData
+
+
+
+
+################################ RECAPITULATION OF WARNING MESSAGES
+
+
+
+
+NO WARNING MESSAGE TO REPORT
+
+
+
+
+################################ INITIAL SETTINGS OF PARAMETERS
+
+
+
+erase.objects TRUE
+erase.graphs TRUE
+script vcf_subfield_title
+run.way SCRIPT
+command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/bin/vcf_subfield_title.R,--args,Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz,cute_little_R_functions.R,vcf_subfield_title_report.txt
+vcf Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz
+cute cute_little_R_functions.R
+log vcf_subfield_title_report.txt
+
+
+
+
+################################ R SYSTEM AND PACKAGES
+
+
+R version 4.1.2 (2021-11-01)
+Platform: x86_64-pc-linux-gnu (64-bit)
+Running under: Ubuntu 20.04.3 LTS
+
+Matrix products: default
+BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
+
+locale:
+ [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
+ [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
+ [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
+ [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
+ [9] LC_ADDRESS=C LC_TELEPHONE=C
+[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+
+attached base packages:
+[1] stats graphics grDevices utils datasets methods base
+
+other attached packages:
+[1] lubridate_1.8.0
+
+loaded via a namespace (and not attached):
+[1] compiler_4.1.2 generics_0.1.2
+
+
+
+
+
+################################ JOB END
+
+TIME: 2022-10-04 14:23:32
+
+TOTAL TIME LAPSE: 0S
+
+
+
diff --git a/example of results/PL_family_WGS_fisher_1664887581/res.tsv.gz b/example of results/PL_family_WGS_fisher_1664893405/res.tsv.gz
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1664887581/res.tsv.gz
rename to example of results/PL_family_WGS_fisher_1664893405/res.tsv.gz
index a289251df4bdb08d9f66a1470bcf0d980ab66d91..54bc9fc858e9ccce8878034154332921e76a5bf9 100644
Binary files a/example of results/PL_family_WGS_fisher_1664887581/res.tsv.gz and b/example of results/PL_family_WGS_fisher_1664893405/res.tsv.gz differ
diff --git a/example of results/PL_family_WGS_fisher_1664887581/res.vcf.gz b/example of results/PL_family_WGS_fisher_1664893405/res.vcf.gz
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/res.vcf.gz
rename to example of results/PL_family_WGS_fisher_1664893405/res.vcf.gz
diff --git a/example of results/PL_family_WGS_fisher_1664887581/res.vcf.gz.tbi b/example of results/PL_family_WGS_fisher_1664893405/res.vcf.gz.tbi
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1664887581/res.vcf.gz.tbi
rename to example of results/PL_family_WGS_fisher_1664893405/res.vcf.gz.tbi
diff --git a/fisher_for_vcf.config b/fisher_for_vcf.config
index 303801668df4d417eac53c887cdb508a62caccee..5ef5d7743fc423044880fe7016f391e7b5d3c87b 100644
--- a/fisher_for_vcf.config
+++ b/fisher_for_vcf.config
@@ -22,7 +22,7 @@ env {
chr_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
//chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
region = "none" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "none" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
- tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required
+ tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required. Warning: use a single space between string
x_lim = "chr1" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
bottom_y_column = "NULL" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file. Then, explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
color_column = "AF" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
diff --git a/fisher_for_vcf.nf b/fisher_for_vcf.nf
index d3e869af29889e30e93b0c6f174d755581bc6054..dbc14e71ac0c572a9fa954071b950969130103d7 100644
--- a/fisher_for_vcf.nf
+++ b/fisher_for_vcf.nf
@@ -190,11 +190,12 @@ process vcf_subfield_title {
output:
file "vcf_info_field_titles.txt" into vcf_info_field_titles_ch
file "vcf_csq_subfield_titles.txt" into vcf_csq_subfield_titles_ch
+ file "vcf_subfield_title_report.txt"
script:
"""
#!/bin/bash -ue
- vcf_subfield_title.R ${vcf} "${cute}" "miami_report.txt"
+ vcf_subfield_title.R ${vcf} "${cute}" "vcf_subfield_title_report.txt"
"""
}
@@ -208,8 +209,8 @@ process fisher {
tuple val(region2), file(vcf) from region_ch.combine(vcf_ch2) // parallelization expected for each value of region_ch
file ped
if(sample_path =~ /.*\.gz$/){file tbi}
- file vcf_info_field_titles from vcf_info_field_titles_ch
- file vcf_csq_subfield_titles from vcf_csq_subfield_titles_ch
+ file vcf_info_field_titles from vcf_info_field_titles_ch.first()
+ file vcf_csq_subfield_titles from vcf_csq_subfield_titles_ch.first()
val tsv_extra_fields
output: