diff --git a/README.md b/README.md
index 15298c848a5c9caccfce719f60ba09117cc186d5..8710596c757beb71bd78f7a0cfd960bdc488c318 100644
--- a/README.md
+++ b/README.md
@@ -203,10 +203,16 @@ Gitlab developers
<br /><br />
## WHAT'S NEW IN
+### v2.1
+
+1) vcf_ficher.nf improved for the whole genome
+
+
### v2.0
1) vcf_ficher.nf added and operationnal
+
### v1.0
1) everything
diff --git a/bin/fisher_lod.py b/bin/fisher_lod.py
index 62d151f918fbf6b577354f79e8f10e419f7e1b30..43cf91da6fc2772706be7be75849300172d364db 100644
--- a/bin/fisher_lod.py
+++ b/bin/fisher_lod.py
@@ -68,10 +68,10 @@ region = sys.argv[3]
# vcf_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
-vcf_path="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
+# vcf_path="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
# ped="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" # functions for slivar
-ped="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.pedigree.txt"
-region="chr7:0-147000000"
+# ped="/mnt/c/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/Dyslexia.pedigree.txt"
+# region=[‘chr7:0-147000000’, ‘chr10:1000000-2000000’]
################################ End Test
@@ -87,6 +87,58 @@ region="chr7:0-147000000"
################################ Functions
+def fisher(v, columns):
+ '''
+ AIM
+ parse vcf and compute fisher
+ WARNINGS
+ ARGUMENTS
+ v: a vcf object from VCF()
+ RETURN
+ a data frame
+ REQUIRED PACKAGES
+ None
+ EXAMPLE
+ fisher(v = vcf, columns = columns)
+ DEBUGGING
+ v = vcf
+ '''
+
+ # je fais 2 dictionnaire pour stocker mes compte d'atteint/non atteint porteurs/non porteurs
+ # dans chaque dictionaire j'associerai a un genotype (clef) un nombre d'individu.
+ aff=dict()
+ una=dict()
+ df2 = pd.DataFrame(columns=columns)
+ # je traite tous les variants qui ont un champ CSQ (annotation VEP)
+ if v.INFO.get('CSQ') is not None:
+ # je recupere quelques annotations
+ gene = v.INFO.get('CSQ').split('|')[3]
+ impact = v.INFO.get('CSQ').split('|')[1]
+ severity = v.INFO.get('CSQ').split('|')[2]
+ # j'initialise une variable qui met permet de garder trace du nombre d'individus pour laquelle j'ai des information pour le variant v courant
+ an=0
+ # pour le variant actuel on parcours la liste des individus (iid) avec les genotype associé (gt), la depth (dp) et la genotyping quality (gq)
+ # gt: 0=HOM_REF ; 1=HET ; 2=UNKNOWN ; 3=HOM_ALT
+ for iid, gt, dp, gq in zip(vcf.samples, v.gt_types, v.format('DP'), v.format('GQ')):
+ # je filtre un depth>=10 et une genotyping quality >=30
+ # on peut decider de baisser le gq a 20 par exemple, c'est jsute une suggestion
+ if dp not in ['.', ''] and int(dp)>=10 and gq not in ['.', ''] and float(gq)>=30:
+ # je met a jour le compte d'individus dans mes dictionnaire aff et una en fonction du phenotype de l'individu courant iid
+ if status[iid]==2:
+ aff[gt]=aff.get(gt,0)+1
+ if status[iid]==1:
+ una[gt]=una.get(gt,0)+1
+ an+=1
+ # une fois que l'on a lu les information pour tous les individus, nous calculons le Fisher
+ # ici c'est porteur (gt 1 ou 3) versus non porteur (gt 0) pour les atteints (aff) versus les non atteint (una)
+ oddsratio, pvalue = stats.fisher_exact([[aff.get(1,0)+aff.get(3,0),aff.get(0,0)],[una.get(1,0)+una.get(3,0),una.get(0,0)]])
+
+ # je met a jour ma dataframe avec les info du variant courant v
+ df2=pd.DataFrame([[v.CHROM, v.POS, v.REF, v.ALT, gene, severity, impact, aff, una, oddsratio, pvalue, -np.log10(pvalue), an]], columns = columns)
+
+ return df2
+
+
################################ End Functions
@@ -125,6 +177,10 @@ random.seed(1)
################ Ignition
+if region == "None":
+ region = None
+else:
+ region = region.strip('[]').replace('"', '').replace(' ', '').split(',')
################ End ignition
@@ -161,43 +217,18 @@ vcf = VCF(vcf_path)
############ modifications of imported tables
+if region is None:
+ for v in vcf:
+ tempo = fisher(v = v, columns = columns)
+ df = df.append(tempo)
+else:
+ for i1 in region :
+ for v in vcf(i1):
+ tempo = fisher(v = v, columns = columns)
+ df = df.append(tempo)
-
-# on parcourt la region du vcf
-for v in vcf(region):
- # je fais 2 dictionnaire pour stocker mes compte d'atteint/non atteint porteurs/non porteurs
- # dans chaque dictionaire j'associerai a un genotype (clef) un nombre d'individu.
- aff=dict()
- una=dict()
- # je traite tous les variants qui ont un champ CSQ (annotation VEP)
- if v.INFO.get('CSQ') is not None:
- # je recupere quelques annotations
- gene = v.INFO.get('CSQ').split('|')[3]
- impact = v.INFO.get('CSQ').split('|')[1]
- severity = v.INFO.get('CSQ').split('|')[2]
- # j'initialise une variable qui met permet de garder trace du nombre d'individus pour laquelle j'ai des information pour le variant v courant
- an=0
- # pour le variant actuel on parcours la liste des individus (iid) avec les genotype associé (gt), la depth (dp) et la genotyping quality (gq)
- # gt: 0=HOM_REF ; 1=HET ; 2=UNKNOWN ; 3=HOM_ALT
- for iid, gt, dp, gq in zip(vcf.samples, v.gt_types, v.format('DP'), v.format('GQ')):
- # je filtre un depth>=10 et une genotyping quality >=30
- # on peut decider de baisser le gq a 20 par exemple, c'est jsute une suggestion
- if dp not in ['.', ''] and int(dp)>=10 and gq not in ['.', ''] and float(gq)>=30:
- # je met a jour le compte d'individus dans mes dictionnaire aff et una en fonction du phenotype de l'individu courant iid
- if status[iid]==2:
- aff[gt]=aff.get(gt,0)+1
- if status[iid]==1:
- una[gt]=una.get(gt,0)+1
- an+=1
- # une fois que l'on a lu les information pour tous les individus, nous calculons le Fisher
- # ici c'est porteur (gt 1 ou 3) versus non porteur (gt 0) pour les atteints (aff) versus les non atteint (una)
- oddsratio, pvalue = stats.fisher_exact([[aff.get(1,0)+aff.get(3,0),aff.get(0,0)],[una.get(1,0)+una.get(3,0),una.get(0,0)]])
-
- # je met a jour ma dataframe avec les info du variant courant v
- df2=pd.DataFrame([[v.CHROM, v.POS, v.REF, v.ALT, gene, severity, impact, aff, una, oddsratio, pvalue, -np.log10(pvalue), an]], columns=columns)
- df = df.append(df2)
# on ecrit la dataframe dans un fichier
-df.to_csv('./'+region.replace(':', '.')+'.fishers.tsv', sep='\t', index=False)
+df.to_csv('./fisher.tsv', sep='\t', index=False)
############ end modifications of imported tables
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/.nextflow.log b/example of results/PL_family_WGS_fisher_1651765929/reports/.nextflow.log
deleted file mode 100644
index 22934b418bbf3496620f53fd400dc82bff5dea70..0000000000000000000000000000000000000000
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/.nextflow.log
+++ /dev/null
@@ -1,55 +0,0 @@
-May-05 17:52:08.848 [main] DEBUG nextflow.cli.Launcher - $> nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git vcf_fisher.nf -c vcf_fisher.config
-May-05 17:52:08.957 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.1
-May-05 17:52:09.002 [main] INFO nextflow.cli.CmdRun - Launching `vcf_fisher.nf` [hopeful_albattani] - revision: 31a5a5ae88
-May-05 17:52:09.017 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/vcf_fisher.config
-May-05 17:52:09.017 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/vcf_fisher.config
-May-05 17:52:09.036 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
-May-05 17:52:09.674 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/.nextflow/plugins
-May-05 17:52:09.677 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
-May-05 17:52:09.680 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
-May-05 17:52:09.696 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
-May-05 17:52:09.698 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
-May-05 17:52:09.701 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
-May-05 17:52:09.711 [main] INFO org.pf4j.AbstractPluginManager - No plugins
-May-05 17:52:09.757 [main] DEBUG nextflow.Session - Session uuid: 177d86c1-39a6-4b64-9575-8df3aad0f71c
-May-05 17:52:09.757 [main] DEBUG nextflow.Session - Run name: hopeful_albattani
-May-05 17:52:09.758 [main] DEBUG nextflow.Session - Executor pool size: 128
-May-05 17:52:09.785 [main] DEBUG nextflow.cli.CmdRun -
- Version: 21.04.1 build 5556
- Created: 14-05-2021 15:20 UTC (17:20 CEST)
- System: Linux 4.18.0-193.70.1.el8_2.x86_64
- Runtime: Groovy 3.0.7 on Java HotSpot(TM) 64-Bit Server VM 13.0.2+8
- Encoding: UTF-8 (UTF-8)
- Process: 2874819@maestro-submit [192.168.148.50]
- CPUs: 128 - Mem: 503.5 GB (3.1 GB) - Swap: 7.8 GB (0)
-May-05 17:52:09.836 [main] DEBUG nextflow.Session - Work-dir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work [nfs]
-May-05 17:52:09.864 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
-May-05 17:52:09.873 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
-May-05 17:52:10.131 [main] DEBUG nextflow.Session - Session start invoked
-May-05 17:52:10.135 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_fisher_1651765929/reports/trace.txt
-May-05 17:52:10.704 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
-May-05 17:52:10.709 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: Backup, WorkflowVersion, fisher
-May-05 17:52:10.801 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:bash` matches label `bash` for process with name WorkflowVersion
-May-05 17:52:10.803 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
-May-05 17:52:10.803 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
-May-05 17:52:10.809 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
-May-05 17:52:10.813 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 2000; pollInterval: 5s; dumpInterval: 5m
-May-05 17:52:10.816 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
-May-05 17:52:10.877 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:python` matches label `python` for process with name fisher
-May-05 17:52:10.879 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
-May-05 17:52:10.879 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
-May-05 17:52:10.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:bash` matches label `bash` for process with name Backup
-May-05 17:52:10.893 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
-May-05 17:52:10.894 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
-May-05 17:52:10.903 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
-May-05 17:52:10.903 [main] DEBUG nextflow.Session - Session await
-May-05 17:52:10.980 [Actor Thread 8] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7; path=/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/singularity/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img
-May-05 17:52:10.981 [Actor Thread 9] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://gmillot/bash-extended_v4.0:gitlab_v8.0; path=/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/singularity/gmillot-bash-extended_v4.0-gitlab_v8.0.img
-May-05 17:52:11.172 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process Backup > jobId: 8332264; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/71/a7820be5977d111caaa05dd8e88b2a
-May-05 17:52:11.175 [Task submitter] INFO nextflow.Session - [71/a7820b] Submitted process > Backup
-May-05 17:52:11.235 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process fisher (1) > jobId: 8332265; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/ff/c595046a853f8f34579ed4b69940b8
-May-05 17:52:11.235 [Task submitter] INFO nextflow.Session - [ff/c59504] Submitted process > fisher (1)
-May-05 17:52:11.289 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process WorkflowVersion > jobId: 8332266; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/94/1d651e54f9e40f79b2f53394cf5ffd
-May-05 17:52:11.290 [Task submitter] INFO nextflow.Session - [94/1d651e] Submitted process > WorkflowVersion
-May-05 17:52:15.848 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 8332264; id: 3; name: Backup; status: COMPLETED; exit: 0; error: -; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/71/a7820be5977d111caaa05dd8e88b2a started: 1651765935829; exited: 2022-05-05T15:52:13.785199Z; ]
-May-05 17:52:15.873 [Task monitor] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=384; maxQueueSize=1152; keepAlive=1m
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/dag.dot b/example of results/PL_family_WGS_fisher_1651765929/reports/dag.dot
deleted file mode 100644
index eecf54f97a08e22989b285d0ba9c00e386983095..0000000000000000000000000000000000000000
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/dag.dot
+++ /dev/null
@@ -1,34 +0,0 @@
-digraph "dag" {
-p0 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
-p7 [label="fisher"];
-p0 -> p7 [label="vcf_ch"];
-
-p1 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
-p7 [label="fisher"];
-p1 -> p7 [label="tbi_ch"];
-
-p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
-p7 [label="fisher"];
-p2 -> p7 [label="ped_ch"];
-
-p4 [shape=point,label="",fixedsize=true,width=0.1];
-p7 [label="fisher"];
-p4 -> p7 [label="region"];
-
-p5 [shape=point,label="",fixedsize=true,width=0.1];
-p7 [label="fisher"];
-p5 -> p7 [label="affected_patients_ch"];
-
-p6 [shape=point,label="",fixedsize=true,width=0.1];
-p7 [label="fisher"];
-p6 -> p7 [label="unaffected_patients_ch"];
-
-p8 [shape=point,label="",fixedsize=true,width=0.1];
-p10 [label="Backup"];
-p8 -> p10 [label="config_file"];
-
-p9 [shape=point,label="",fixedsize=true,width=0.1];
-p10 [label="Backup"];
-p9 -> p10 [label="log_file"];
-
-}
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/trace.txt b/example of results/PL_family_WGS_fisher_1651765929/reports/trace.txt
deleted file mode 100644
index 6b562cf86c1566f93800cf37bee0a1d966a638fb..0000000000000000000000000000000000000000
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/trace.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
-3 71/a7820b 8332264 Backup COMPLETED 0 2022-05-05 17:52:11.171 4.7s 14ms 5.0% 0 0 121.7 KB 1.5 KB
-1 94/1d651e 8332266 WorkflowVersion COMPLETED 0 2022-05-05 17:52:11.289 4.7s 126ms 10.0% 0 0 151 KB 3.3 KB
-2 ff/c59504 8332265 fisher (1) COMPLETED 0 2022-05-05 17:52:11.235 44.6s 38.9s 100.5% 118.8 MB 1.4 GB 16.7 MB 5.8 MB
diff --git a/example of results/PL_family_WGS_fisher_1651765929/chr1.0-147000000.fishers.tsv b/example of results/PL_family_WGS_fisher_1651770212/fisher.tsv
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1651765929/chr1.0-147000000.fishers.tsv
rename to example of results/PL_family_WGS_fisher_1651770212/fisher.tsv
diff --git a/example of results/PL_family_WGS_fisher_1651770212/reports/.nextflow.log b/example of results/PL_family_WGS_fisher_1651770212/reports/.nextflow.log
new file mode 100644
index 0000000000000000000000000000000000000000..4fc808e7cfd53afef8a8ff8572612de866402744
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1651770212/reports/.nextflow.log
@@ -0,0 +1,55 @@
+May-05 19:03:31.627 [main] DEBUG nextflow.cli.Launcher - $> nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git vcf_fisher.nf -c vcf_fisher.config
+May-05 19:03:31.732 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.1
+May-05 19:03:31.752 [main] INFO nextflow.cli.CmdRun - Launching `vcf_fisher.nf` [admiring_woese] - revision: ed4d485e57
+May-05 19:03:31.766 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/vcf_fisher.config
+May-05 19:03:31.766 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/vcf_fisher.config
+May-05 19:03:31.784 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
+May-05 19:03:32.398 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/.nextflow/plugins
+May-05 19:03:32.399 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
+May-05 19:03:32.401 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
+May-05 19:03:32.407 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
+May-05 19:03:32.408 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
+May-05 19:03:32.412 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
+May-05 19:03:32.419 [main] INFO org.pf4j.AbstractPluginManager - No plugins
+May-05 19:03:32.454 [main] DEBUG nextflow.Session - Session uuid: 8026e894-6648-4984-a48c-c34e91f0ba7f
+May-05 19:03:32.454 [main] DEBUG nextflow.Session - Run name: admiring_woese
+May-05 19:03:32.455 [main] DEBUG nextflow.Session - Executor pool size: 128
+May-05 19:03:32.475 [main] DEBUG nextflow.cli.CmdRun -
+ Version: 21.04.1 build 5556
+ Created: 14-05-2021 15:20 UTC (17:20 CEST)
+ System: Linux 4.18.0-193.70.1.el8_2.x86_64
+ Runtime: Groovy 3.0.7 on Java HotSpot(TM) 64-Bit Server VM 13.0.2+8
+ Encoding: UTF-8 (UTF-8)
+ Process: 2965103@maestro-submit [192.168.148.50]
+ CPUs: 128 - Mem: 503.5 GB (3.8 GB) - Swap: 7.8 GB (0)
+May-05 19:03:32.509 [main] DEBUG nextflow.Session - Work-dir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work [nfs]
+May-05 19:03:32.528 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
+May-05 19:03:32.537 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
+May-05 19:03:32.661 [main] DEBUG nextflow.Session - Session start invoked
+May-05 19:03:32.665 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_fisher_1651770212/reports/trace.txt
+May-05 19:03:33.023 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
+May-05 19:03:33.029 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: Backup, WorkflowVersion, fisher
+May-05 19:03:33.122 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:bash` matches label `bash` for process with name WorkflowVersion
+May-05 19:03:33.124 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
+May-05 19:03:33.124 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
+May-05 19:03:33.131 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
+May-05 19:03:33.136 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 2000; pollInterval: 5s; dumpInterval: 5m
+May-05 19:03:33.139 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
+May-05 19:03:33.210 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:python` matches label `python` for process with name fisher
+May-05 19:03:33.212 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
+May-05 19:03:33.212 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
+May-05 19:03:33.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:bash` matches label `bash` for process with name Backup
+May-05 19:03:33.228 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
+May-05 19:03:33.228 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
+May-05 19:03:33.238 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
+May-05 19:03:33.239 [main] DEBUG nextflow.Session - Session await
+May-05 19:03:33.276 [Actor Thread 8] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://gmillot/bash-extended_v4.0:gitlab_v8.0; path=/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/singularity/gmillot-bash-extended_v4.0-gitlab_v8.0.img
+May-05 19:03:33.276 [Actor Thread 9] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7; path=/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/singularity/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img
+May-05 19:03:33.415 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process Backup > jobId: 8337568; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/13/c497a1aaa7f45ef6174fd3d4a64e78
+May-05 19:03:33.418 [Task submitter] INFO nextflow.Session - [13/c497a1] Submitted process > Backup
+May-05 19:03:33.455 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process fisher (1) > jobId: 8337569; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/cc/f21157a91575348cca5ecc2f72da4b
+May-05 19:03:33.456 [Task submitter] INFO nextflow.Session - [cc/f21157] Submitted process > fisher (1)
+May-05 19:03:33.491 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process WorkflowVersion > jobId: 8337570; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/65/f5debad3f5634120c0b2449c7ad7c9
+May-05 19:03:33.491 [Task submitter] INFO nextflow.Session - [65/f5deba] Submitted process > WorkflowVersion
+May-05 19:03:38.159 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 8337568; id: 3; name: Backup; status: COMPLETED; exit: 0; error: -; workDir: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/work/13/c497a1aaa7f45ef6174fd3d4a64e78 started: 1651770218147; exited: 2022-05-05T17:03:34.6453Z; ]
+May-05 19:03:38.176 [Task monitor] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=384; maxQueueSize=1152; keepAlive=1m
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/Log_info.txt b/example of results/PL_family_WGS_fisher_1651770212/reports/Log_info.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1651765929/reports/Log_info.txt
rename to example of results/PL_family_WGS_fisher_1651770212/reports/Log_info.txt
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/Run_info.txt b/example of results/PL_family_WGS_fisher_1651770212/reports/Run_info.txt
similarity index 93%
rename from example of results/PL_family_WGS_fisher_1651765929/reports/Run_info.txt
rename to example of results/PL_family_WGS_fisher_1651770212/reports/Run_info.txt
index 70b96c5a383b3d912347c573cb9aac6441eb3a55..02fea6e0dbcec53ffd3e50b88deaf9e63d8ff006 100644
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/Run_info.txt
+++ b/example of results/PL_family_WGS_fisher_1651770212/reports/Run_info.txt
@@ -4,7 +4,7 @@ Cmd line: nextflow run --modules /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gens
execution mode: slurm
loaded modules (according to specification by the user thanks to the --modules argument of main.nf): /opt/gensoft/exe/java/13.0.2/bin/java,/opt/gensoft/exe/singularity/3.8.3/bin/singularity,/opt/gensoft/exe/git/2.25.0/bin/git
Manifest's pipeline version: null
-result path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_fisher_1651765929
+result path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_fisher_1651770212
nextflow version: 21.04.1
@@ -17,5 +17,5 @@ workDir (directory where tasks temporary files are created): /pasteur/zeus/proje
USER VARIABLES:
-out_path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_fisher_1651765929
+out_path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/results/PL_family_WGS_fisher_1651770212
sample_path: /pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz
diff --git a/example of results/PL_family_WGS_fisher_1651770212/reports/dag.dot b/example of results/PL_family_WGS_fisher_1651770212/reports/dag.dot
new file mode 100644
index 0000000000000000000000000000000000000000..4623d332f99ff03dc8b84a7ef158b8e04c669ff0
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1651770212/reports/dag.dot
@@ -0,0 +1,26 @@
+digraph "dag" {
+p0 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
+p5 [label="fisher"];
+p0 -> p5 [label="vcf_ch"];
+
+p1 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
+p5 [label="fisher"];
+p1 -> p5 [label="tbi_ch"];
+
+p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
+p5 [label="fisher"];
+p2 -> p5 [label="ped_ch"];
+
+p4 [shape=point,label="",fixedsize=true,width=0.1];
+p5 [label="fisher"];
+p4 -> p5 [label="region"];
+
+p6 [shape=point,label="",fixedsize=true,width=0.1];
+p8 [label="Backup"];
+p6 -> p8 [label="config_file"];
+
+p7 [shape=point,label="",fixedsize=true,width=0.1];
+p8 [label="Backup"];
+p7 -> p8 [label="log_file"];
+
+}
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/report.html b/example of results/PL_family_WGS_fisher_1651770212/reports/report.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1651765929/reports/report.html
rename to example of results/PL_family_WGS_fisher_1651770212/reports/report.html
index db23f17035ebd43ad0e2bb3d9e433ee7611bcdf8..d7235e059ed170de72ee68588c1a0efd03819a67 100644
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/report.html
+++ b/example of results/PL_family_WGS_fisher_1651770212/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 [hopeful_albattani]">
+ <meta name="description" content="Nextflow workflow report for run id [admiring_woese]">
<meta name="author" content="Paolo Di Tommaso, Phil Ewels">
<link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
- <title>[hopeful_albattani] Nextflow Workflow Report</title>
+ <title>[admiring_woese] 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">
- [hopeful_albattani]
+ [admiring_woese]
</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>[hopeful_albattani]</samp> </h2>
+ <h2 class="text-muted mb-4"><samp>[admiring_woese]</samp> </h2>
<div class="alert alert-success mb-4">
@@ -157,8 +157,8 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
<dl>
<dt>Run times</dt>
<dd>
- <span id="workflow_start">05-May-2022 17:52:09</span> - <span id="workflow_complete">05-May-2022 17:52:55</span>
- (<span id="completed_fromnow"></span>duration: <strong>46s</strong>)
+ <span id="workflow_start">05-May-2022 19:03:32</span> - <span id="workflow_complete">05-May-2022 19:04:28</span>
+ (<span id="completed_fromnow"></span>duration: <strong>55.6s</strong>)
</dd>
<dl>
@@ -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>31a5a5ae88a24723422cba63e0151766</code></dd>
+ <dd class="col-sm-9"><code>ed4d485e575f96e8d8eb2ae616516616</code></dd>
<dt class="col-sm-3">Workflow session</dt>
- <dd class="col-sm-9"><code>177d86c1-39a6-4b64-9575-8df3aad0f71c</code></dd>
+ <dd class="col-sm-9"><code>8026e894-6648-4984-a48c-c34e91f0ba7f</code></dd>
@@ -1029,7 +1029,7 @@ $(function() {
// Nextflow report data
window.data = { "trace":[
-{"task_id":"3","hash":"71\/a7820b","native_id":"8332264","process":"Backup","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/14985_loot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1651765931171","start":"1651765935829","complete":"1651765935847","duration":"4676","realtime":"14","%cpu":"5.0","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"124604","wchar":"1526","syscr":"189","syscw":"32","read_bytes":"246784","write_bytes":"4096","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/71\/a7820be5977d111caaa05dd8e88b2a","script":"\n echo -e \"full .nextflow.log is in: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nregion=chr1:0-147000000\naffected_patients=C0011JZ C0011K2 C0011K3 C0011KA IP00FNP IP00FNW IP00FNY\nunaffected_patients=C0011JY C0011K1 C0011K5 C0011KB\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651765929\nsystem_exec=slurm\nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"2","hash":"ff\/c59504","native_id":"8332265","process":"fisher","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/14985_loot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1651765931235","start":"1651765935908","complete":"1651765975845","duration":"44610","realtime":"38889","%cpu":"100.5","%mem":"0.0","rss":"124571648","vmem":"1503744000","peak_rss":"124571648","peak_vmem":"1503776768","rchar":"17546968","wchar":"6080438","syscr":"2052","syscw":"19244","read_bytes":"36590592","write_bytes":"1056768","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/ff\/c595046a853f8f34579ed4b69940b8","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt chr1:0-147000000\n ","scratch":"-","queue":"hubbioit","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nregion=chr1:0-147000000\naffected_patients=C0011JZ C0011K2 C0011K3 C0011KA IP00FNP IP00FNW IP00FNY\nunaffected_patients=C0011JY C0011K1 C0011K5 C0011KB\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651765929\nsystem_exec=slurm\nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"2095","inv_ctxt":"255"},{"task_id":"1","hash":"94\/1d651e","native_id":"8332266","process":"WorkflowVersion","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/14985_loot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1651765931289","start":"1651765935955","complete":"1651765935966","duration":"4677","realtime":"126","%cpu":"10.0","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"154631","wchar":"3359","syscr":"234","syscw":"59","read_bytes":"1082368","write_bytes":"40960","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/94\/1d651e54f9e40f79b2f53394cf5ffd","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron 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 \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron 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 --modules \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git vcf_fisher.nf -c vcf_fisher.config\" >> Run_info.txt\n echo \"execution mode\": slurm >> Run_info.txt\n modules=\/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git # 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)\": \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651765929\" >> Run_info.txt\n echo \"nextflow version: 21.04.1\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nprojectDir (directory where the main.nf script is located): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nworkDir (directory where tasks temporary files are created): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651765929\\nsample_path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nregion=chr1:0-147000000\naffected_patients=C0011JZ C0011K2 C0011K3 C0011KA IP00FNP IP00FNW IP00FNY\nunaffected_patients=C0011JY C0011K1 C0011K5 C0011KB\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651765929\nsystem_exec=slurm\nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"}], "summary":[{"cpuUsage":{"mean":0.31,"min":0.31,"q1":0.31,"q2":0.31,"q3":0.31,"max":0.31,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"process":"Backup","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":124604,"min":124604,"q1":124604,"q2":124604,"q3":124604,"max":124604,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"cpu":{"mean":5,"min":5,"q1":5,"q2":5,"q3":5,"max":5,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"time":{"mean":14,"min":14,"q1":14,"q2":14,"q3":14,"max":14,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"writes":{"mean":1526,"min":1526,"q1":1526,"q2":1526,"q3":1526,"max":1526,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"}},{"cpuUsage":{"mean":0.63,"min":0.63,"q1":0.63,"q2":0.63,"q3":0.63,"max":0.63,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"process":"WorkflowVersion","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":154631,"min":154631,"q1":154631,"q2":154631,"q3":154631,"max":154631,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"cpu":{"mean":10,"min":10,"q1":10,"q2":10,"q3":10,"max":10,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"time":{"mean":126,"min":126,"q1":126,"q2":126,"q3":126,"max":126,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"writes":{"mean":3359,"min":3359,"q1":3359,"q2":3359,"q3":3359,"max":3359,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"}},{"cpuUsage":{"mean":6.28,"min":6.28,"q1":6.28,"q2":6.28,"q3":6.28,"max":6.28,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"process":"fisher","mem":{"mean":124571648,"min":124571648,"q1":124571648,"q2":124571648,"q3":124571648,"max":124571648,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"memUsage":{"mean":0.18,"min":0.18,"q1":0.18,"q2":0.18,"q3":0.18,"max":0.18,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"timeUsage":null,"vmem":{"mean":1503776768,"min":1503776768,"q1":1503776768,"q2":1503776768,"q3":1503776768,"max":1503776768,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"reads":{"mean":17546968,"min":17546968,"q1":17546968,"q2":17546968,"q3":17546968,"max":17546968,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"cpu":{"mean":100.5,"min":100.5,"q1":100.5,"q2":100.5,"q3":100.5,"max":100.5,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"time":{"mean":38889,"min":38889,"q1":38889,"q2":38889,"q3":38889,"max":38889,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"writes":{"mean":6080438,"min":6080438,"q1":6080438,"q2":6080438,"q3":6080438,"max":6080438,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"}}] };
+{"task_id":"3","hash":"13\/c497a1","native_id":"8337568","process":"Backup","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/14985_loot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1651770213415","start":"1651770218147","complete":"1651770218159","duration":"4744","realtime":"12","%cpu":"36.5","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"124609","wchar":"1527","syscr":"189","syscw":"32","read_bytes":"246784","write_bytes":"4096","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/13\/c497a1aaa7f45ef6174fd3d4a64e78","script":"\n echo -e \"full .nextflow.log is in: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nregion=[\'chr7:0-147000000\', \'chr1:0-2000000\']\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651770212\nsystem_exec=slurm\nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"2","hash":"cc\/f21157","native_id":"8337569","process":"fisher","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/14985_loot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1651770213455","start":"1651770218197","complete":"1651770268153","duration":"54698","realtime":"48955","%cpu":"105.9","%mem":"0.0","rss":"124624896","vmem":"1503830016","peak_rss":"124919808","peak_vmem":"1503993856","rchar":"17547622","wchar":"6158163","syscr":"2053","syscw":"19492","read_bytes":"34763776","write_bytes":"1056768","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/cc\/f21157a91575348cca5ecc2f72da4b","script":"\n #!\/bin\/bash -ue\n fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt [\'chr7:0-147000000\', \'chr1:0-2000000\']\n ","scratch":"-","queue":"hubbioit","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nregion=[\'chr7:0-147000000\', \'chr1:0-2000000\']\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651770212\nsystem_exec=slurm\nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"1438","inv_ctxt":"271"},{"task_id":"1","hash":"65\/f5deba","native_id":"8337570","process":"WorkflowVersion","module":"-","container":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/14985_loot\/singularity\/gmillot-bash-extended_v4.0-gitlab_v8.0.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1651770213491","start":"1651770218229","complete":"1651770218239","duration":"4748","realtime":"66","%cpu":"34.1","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"154137","wchar":"3355","syscr":"234","syscw":"59","read_bytes":"1082368","write_bytes":"40960","attempt":"1","workdir":"\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\/65\/f5debad3f5634120c0b2449c7ad7c9","script":"\n echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron 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 \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron 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 --modules \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git vcf_fisher.nf -c vcf_fisher.config\" >> Run_info.txt\n echo \"execution mode\": slurm >> Run_info.txt\n modules=\/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git # 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 $modules ]] ; then\n echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\": \/opt\/gensoft\/exe\/java\/13.0.2\/bin\/java,\/opt\/gensoft\/exe\/singularity\/3.8.3\/bin\/singularity,\/opt\/gensoft\/exe\/git\/2.25.0\/bin\/git >> Run_info.txt\n fi\n echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n echo \"result path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651770212\" >> Run_info.txt\n echo \"nextflow version: 21.04.1\" >> Run_info.txt\n echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nprojectDir (directory where the main.nf script is located): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\\nworkDir (directory where tasks temporary files are created): \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/work\" >> Run_info.txt\n echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651770212\\nsample_path: \/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n ","scratch":"-","queue":"hubbioit","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/dataset\/Dyslexia.pedigree.txt\nregion=[\'chr7:0-147000000\', \'chr1:0-2000000\']\nout_path=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/results\/PL_family_WGS_fisher_1651770212\nsystem_exec=slurm\nPATH=\/pasteur\/zeus\/projets\/p01\/BioIT\/gmillot\/08002_bourgeron\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"}], "summary":[{"cpuUsage":{"mean":2.28,"min":2.28,"q1":2.28,"q2":2.28,"q3":2.28,"max":2.28,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"process":"Backup","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":124609,"min":124609,"q1":124609,"q2":124609,"q3":124609,"max":124609,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"cpu":{"mean":36.5,"min":36.5,"q1":36.5,"q2":36.5,"q3":36.5,"max":36.5,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"time":{"mean":12,"min":12,"q1":12,"q2":12,"q3":12,"max":12,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"},"writes":{"mean":1527,"min":1527,"q1":1527,"q2":1527,"q3":1527,"max":1527,"minLabel":"Backup","maxLabel":"Backup","q1Label":"Backup","q2Label":"Backup","q3Label":"Backup"}},{"cpuUsage":{"mean":2.13,"min":2.13,"q1":2.13,"q2":2.13,"q3":2.13,"max":2.13,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"process":"WorkflowVersion","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":154137,"min":154137,"q1":154137,"q2":154137,"q3":154137,"max":154137,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"cpu":{"mean":34.1,"min":34.1,"q1":34.1,"q2":34.1,"q3":34.1,"max":34.1,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"time":{"mean":66,"min":66,"q1":66,"q2":66,"q3":66,"max":66,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"},"writes":{"mean":3355,"min":3355,"q1":3355,"q2":3355,"q3":3355,"max":3355,"minLabel":"WorkflowVersion","maxLabel":"WorkflowVersion","q1Label":"WorkflowVersion","q2Label":"WorkflowVersion","q3Label":"WorkflowVersion"}},{"cpuUsage":{"mean":6.62,"min":6.62,"q1":6.62,"q2":6.62,"q3":6.62,"max":6.62,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"process":"fisher","mem":{"mean":124919808,"min":124919808,"q1":124919808,"q2":124919808,"q3":124919808,"max":124919808,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"memUsage":{"mean":0.18,"min":0.18,"q1":0.18,"q2":0.18,"q3":0.18,"max":0.18,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"timeUsage":null,"vmem":{"mean":1503993856,"min":1503993856,"q1":1503993856,"q2":1503993856,"q3":1503993856,"max":1503993856,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"reads":{"mean":17547622,"min":17547622,"q1":17547622,"q2":17547622,"q3":17547622,"max":17547622,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"cpu":{"mean":105.9,"min":105.9,"q1":105.9,"q2":105.9,"q3":105.9,"max":105.9,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"time":{"mean":48955,"min":48955,"q1":48955,"q2":48955,"q3":48955,"max":48955,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"},"writes":{"mean":6158163,"min":6158163,"q1":6158163,"q2":6158163,"q3":6158163,"max":6158163,"minLabel":"fisher (1)","maxLabel":"fisher (1)","q1Label":"fisher (1)","q2Label":"fisher (1)","q3Label":"fisher (1)"}}] };
</script>
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/timeline.html b/example of results/PL_family_WGS_fisher_1651770212/reports/timeline.html
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1651765929/reports/timeline.html
rename to example of results/PL_family_WGS_fisher_1651770212/reports/timeline.html
index 48604f092dddaec3b301d632c8c61d2a3244ee0e..08d6be6022d5eec818f0ab03b8a7e9d261f9ced7 100644
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/timeline.html
+++ b/example of results/PL_family_WGS_fisher_1651770212/reports/timeline.html
@@ -205,13 +205,13 @@ $(function() {
// Nextflow report data
window.data = {
- "elapsed": "46.3s",
- "beginningMillis": 1651765930151,
- "endingMillis": 1651765976490,
+ "elapsed": "56.1s",
+ "beginningMillis": 1651770212675,
+ "endingMillis": 1651770268736,
"processes": [
- {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1651765931171, "ending_time": 1651765935829}, {"starting_time": 1651765935829, "ending_time": 1651765935843, "label": "4.7s \/ 0"}, {"starting_time": 1651765935843, "ending_time": 1651765935847}]},
- {"label": "fisher (1)", "cached": false, "index": 1, "times": [{"starting_time": 1651765931235, "ending_time": 1651765935908}, {"starting_time": 1651765935908, "ending_time": 1651765974797, "label": "44.6s \/ 118.8 MB"}, {"starting_time": 1651765974797, "ending_time": 1651765975845}]},
- {"label": "WorkflowVersion", "cached": false, "index": 2, "times": [{"starting_time": 1651765931289, "ending_time": 1651765935955}, {"starting_time": 1651765935955, "ending_time": 1651765936081, "label": "4.7s \/ 0"}]}
+ {"label": "Backup", "cached": false, "index": 0, "times": [{"starting_time": 1651770213415, "ending_time": 1651770218147}, {"starting_time": 1651770218147, "ending_time": 1651770218159, "label": "4.7s \/ 0"}]},
+ {"label": "fisher (1)", "cached": false, "index": 1, "times": [{"starting_time": 1651770213455, "ending_time": 1651770218197}, {"starting_time": 1651770218197, "ending_time": 1651770267152, "label": "54.7s \/ 119.1 MB"}, {"starting_time": 1651770267152, "ending_time": 1651770268153}]},
+ {"label": "WorkflowVersion", "cached": false, "index": 2, "times": [{"starting_time": 1651770213491, "ending_time": 1651770218229}, {"starting_time": 1651770218229, "ending_time": 1651770218295, "label": "4.7s \/ 0"}]}
]
}
;
diff --git a/example of results/PL_family_WGS_fisher_1651770212/reports/trace.txt b/example of results/PL_family_WGS_fisher_1651770212/reports/trace.txt
new file mode 100644
index 0000000000000000000000000000000000000000..deb56150f54a89887907a07f8f91408b68167d88
--- /dev/null
+++ b/example of results/PL_family_WGS_fisher_1651770212/reports/trace.txt
@@ -0,0 +1,4 @@
+task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
+3 13/c497a1 8337568 Backup COMPLETED 0 2022-05-05 19:03:33.415 4.7s 12ms 36.5% 0 0 121.7 KB 1.5 KB
+1 65/f5deba 8337570 WorkflowVersion COMPLETED 0 2022-05-05 19:03:33.491 4.7s 66ms 34.1% 0 0 150.5 KB 3.3 KB
+2 cc/f21157 8337569 fisher (1) COMPLETED 0 2022-05-05 19:03:33.455 54.7s 49s 105.9% 119.1 MB 1.4 GB 16.7 MB 5.9 MB
diff --git a/example of results/PL_family_WGS_fisher_1651765929/reports/vcf_fisher.config b/example of results/PL_family_WGS_fisher_1651770212/reports/vcf_fisher.config
similarity index 95%
rename from example of results/PL_family_WGS_fisher_1651765929/reports/vcf_fisher.config
rename to example of results/PL_family_WGS_fisher_1651770212/reports/vcf_fisher.config
index d955e1d210595bf037fd6e9a128e0ecb86598d57..ad9e88c0ae62c2e052764e584175a6ab596c347d 100644
--- a/example of results/PL_family_WGS_fisher_1651765929/reports/vcf_fisher.config
+++ b/example of results/PL_family_WGS_fisher_1651770212/reports/vcf_fisher.config
@@ -19,9 +19,7 @@ env {
sample_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
//Warning: do not write the out_path now. See below. If written here, the one below is not considered"
ped_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" // functions for slivar
- region="chr1:0-147000000" // region to parse. Write for instance 'chr10:0-2538030'
- affected_patients="C0011JZ C0011K2 C0011K3 C0011KA IP00FNP IP00FNW IP00FNY" // Warning: mandatory space separators
- unaffected_patients="C0011JY C0011K1 C0011K5 C0011KB" // Warning: mandatory space separators
+ region="['chr7:0-147000000', 'chr1:0-2000000']" // Warning : replace eval() by ast.literal_eval() from ast package in the main py code. region to parse. Write "['chr7:0-147000000', 'chr10:1000000-2000000']" for a single region, "['chr7:0-147000000', 'chr10:1000000-2000000']" if two regions nad "None" for the complete genome
}
//////// end variables that will be used only in the main.nf
diff --git a/vcf_fisher.config b/vcf_fisher.config
index 0bf6e7150ece2aeda8128dc8d184ba16f3c62554..ad9e88c0ae62c2e052764e584175a6ab596c347d 100644
--- a/vcf_fisher.config
+++ b/vcf_fisher.config
@@ -19,9 +19,7 @@ env {
sample_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
//Warning: do not write the out_path now. See below. If written here, the one below is not considered"
ped_path="/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" // functions for slivar
- region="chr7:0-147000000" // region to parse. Write for instance 'chr10:0-2538030'
- affected_patients="C0011JZ C0011K2 C0011K3 C0011KA IP00FNP IP00FNW IP00FNY" // Warning: mandatory space separators
- unaffected_patients="C0011JY C0011K1 C0011K5 C0011KB" // Warning: mandatory space separators
+ region="['chr7:0-147000000', 'chr1:0-2000000']" // Warning : replace eval() by ast.literal_eval() from ast package in the main py code. region to parse. Write "['chr7:0-147000000', 'chr10:1000000-2000000']" for a single region, "['chr7:0-147000000', 'chr10:1000000-2000000']" if two regions nad "None" for the complete genome
}
//////// end variables that will be used only in the main.nf
diff --git a/vcf_fisher.nf b/vcf_fisher.nf
index 24180816b4ce0601870105751d67c99744df03eb..a319b076720f1cad08d80cdd5bcdb5eb7c61a001 100644
--- a/vcf_fisher.nf
+++ b/vcf_fisher.nf
@@ -45,11 +45,6 @@ vcf_ch = Channel.fromPath("${sample_path}", checkIfExists: false) // I could use
tbi_ch = Channel.fromPath("${sample_path}.tbi", checkIfExists: false) // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
ped_ch = Channel.fromPath("${ped_path}", checkIfExists: false) // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
-affected_patients_ch = Channel.value("${affected_patients}")
-unaffected_patients_ch = Channel.value("${unaffected_patients}")
-patient_ch = Channel.value(["${affected_patients}", "${unaffected_patients}"]) // create two entries, see https://www.nextflow.io/docs/latest/channel.html#from
-patient_name_ch = Channel.value(["affected_patients", "unaffected_patients"]) // create two entries, see https://www.nextflow.io/docs/latest/channel.html#from
-
//// end used once
//////// end Channels
@@ -125,9 +120,6 @@ process fisher {
file ped from ped_ch
file tbi from tbi_ch
val region
- val affected_patients from affected_patients_ch
- val unaffected_patients from unaffected_patients_ch
- // see the scope for the use of affected_patients which is already a variable from .config file
output:
file "*.tsv"