diff --git a/README.md b/README.md
index 74382c69f9ad4c2c61daf580cf79ba54700c10fe..6b4e3ae232577bcaa227dd458d7ba8e74fc0648e 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
| usage | dependencies |
| --- | --- |
-| [](https://www.nextflow.io/) | [](https://github.com/nextflow-io/nextflow) |
+| [](https://www.nextflow.io/) | [](https://github.com/nextflow-io/nextflow) |
| [-green?style=plastic)](https://www.gnu.org/licenses) | |
<br /><br />
@@ -28,6 +28,7 @@
- Compute the two-sided Fisher exact test statistics (score) and p values from a vcf annotated file made of patient and control cases.
+- Odds ratio used is (n11/n12)/(n21/n22) = (n11\*n22)/(n12\*n21) with:<br /><ul><li>n11 = nHET_aff + nHOM_ALT_aff (carrier in aff)<br /></li><li>n12 = nHOM_REF_aff (non-carrier in aff)<br /></li><li>n21 = nHET_unaff + nHOM_ALT_unaff (carrier in unaff)<br /></li><li>n22 = nHOM_REF_unaff (non-carrier in unaff)<br /></li>OR > 1 meaning OR in favor of HET+HOM_ALT/aff versus HET+HOM_ALT/unaff
- Return a res.tsv file and a Miami plot.
- The tsv file can include fields and sub-fields of the vcf file in different columns. See the tsv_extra_fields parameter of the nextflow.config file, as well as the OUTPUT section below.
- Return also a res.vcf file made from the res.tsv file, mimicing a VCF file, i.e., with the inital header of the .vcf and with the fisher results added in the INFO section.
@@ -295,6 +296,12 @@ The developers & maintainers of the mentioned softwares and packages, including:
<br /><br />
## WHAT'S NEW IN
+### v3.0
+
+- DSL1 -> DSL2.
+- Two-sided test Fisher test added but remain to be control the resulting p value.
+
+
### v2.5
- .config improved
diff --git a/bin/fisher_lod.py b/bin/fisher_lod.py
index f4565189d5b36fbdcb570707786d0346c0b630c6..f7794222e7ba59a9dfc18c0fe781edcf8f4375bc 100644
--- a/bin/fisher_lod.py
+++ b/bin/fisher_lod.py
@@ -160,7 +160,7 @@ csq_subfield_pos = [26]
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)]])
+ 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)]], alternative='two-sided')
# filling a one row data frame with or without adding
tempo_csq = v.INFO.get('CSQ').split(',') # number of fields in CSQ (comma sep), i.e., nb of rows
diff --git a/main.nf b/main.nf
index 80911d0391beac0cc73f79987a3ed9fe5db20ed0..9df947798b23c621bccfa7996dca11fd1235c688 100644
--- a/main.nf
+++ b/main.nf
@@ -1,4 +1,4 @@
-nextflow.enable.dsl=1
+nextflow.enable.dsl=2
/*
#########################################################################
## ##
@@ -13,173 +13,21 @@ nextflow.enable.dsl=1
*/
-//////// Options of nextflow run
-
-params.modules = ""
-
-//////// end Options of nextflow run
-
-
-//////// Variables
-
-// from the nextflow.config file
-config_file = file("${projectDir}/fisher_for_vcf.config") // file() create a path object necessary o then create the file
-log_file = file("${launchDir}/.nextflow.log")
-
-// files objects created in order to use .exists() to test the path
-chr = file(chr_path)
-ped = file(ped_path)
-cute = file(cute_path) // converted to file path directly to use it as a constant
-out = file(out_path)
-// end from the nextflow.config file
-
-// from parameters (options of the nexflow command line)
-modules = params.modules // remove the dot -> can be used in bash scripts
-// end from parameters (options of the nexflow command line)
-
-
-//////// end Variables
-
-
-//////// Variables from config.file that need to be modified
-
-
-if(x_lim == 'whole' || (x_lim == 'region' && region == 'none')){ // for the miami plot
- x_lim_val = "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM" // I have added both notations "chr23", "chr24", "chr25" or "chrY", "chrX", "chrM" because either one or the other can be used in a VCF file
-}else if(x_lim == 'region'){
- x_lim_val = region
-}else{
- x_lim_val = x_lim // value for the miami plot
-}
-
-//////// end Variables from config.file that need to be modified
-
-
-//////// Channels
-
-
-Channel.fromPath("${sample_path}", checkIfExists: false).into{vcf_ch1 ; vcf_ch2 ; vcf_ch3} // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
-if(region == 'none'){ // for combine below for parallelization of the fisher process
- region_ch = Channel.from("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chr23", "chr24", "chr25", "chrY", "chrX", "chrM") // I have added both notations "chr23", "chr24", "chr25" or "chrY", "chrX", "chrM" because either one or the other can be used in a VCF file
-}else{
- if(region =~ /,/){
- tempo = region.replaceAll(':.+,', ',')
- }else{
- tempo = region
- }
- tempo2 = tempo.replaceAll(':.+$', '')
- tempo3 = tempo2.replaceAll(' ', '')
- tempo4 = tempo3.split(",") // .split(",") split according to comma and create an array https://www.tutorialspoint.com/groovy/groovy_split.htm
- region_ch = Channel.from(tempo4)
-}
-
-
-//////// end Channels
-
-
-
-//////// Checks
-
-sample_path_test = file("${sample_path}") // because is a channel
-tbi_test = file("${sample_path}.tbi")
-
-def file_exists1 = sample_path_test.exists()
-if( ! file_exists1){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID sample_path PARAMETER IN nextflow.config FILE: ${sample_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
-}else if(sample_path =~ /.*\.gz$/){
- def file_exists2 = tbi_test.exists()
- if( ! file_exists2){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID .tbi FILE ASSOCIATED TO sample_path PARAMETER IN nextflow.config FILE: ${sample_path}.tbi\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\nOTHERWISE, USE tabix -p vcf <NAME>.vcf TO INDEX THE .gz FILE\n\n========\n\n"
- }else{
- tbi = file("${sample_path}.tbi")
- }
-}
-def file_exists3 = ped.exists()
-if( ! file_exists3){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ped_path PARAMETER IN nextflow.config FILE: ${ped_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
-}
-def file_exists4 = chr.exists()
-if( ! file_exists4){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID chr_path PARAMETER IN nextflow.config FILE: ${chr_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
-}
-
-if( ! region in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID region PARAMETER IN nextflow.config FILE:\n${region}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! tsv_extra_fields in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID tsv_extra_fields PARAMETER IN nextflow.config FILE:\n${tsv_extra_fields}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! x_lim in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID x_lim PARAMETER IN nextflow.config FILE:\n${x_lim}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! vgrid in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID vgrid PARAMETER IN nextflow.config FILE:\n${vgrid}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! top_y_column in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID top_y_column PARAMETER IN nextflow.config FILE:\n${top_y_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! bottom_y_column in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID bottom_y_column PARAMETER IN nextflow.config FILE:\n${bottom_y_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! color_column in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID color_column PARAMETER IN nextflow.config FILE:\n${color_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_lim1 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim1 PARAMETER IN nextflow.config FILE:\n${y_lim1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_lim2 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim2 PARAMETER IN nextflow.config FILE:\n${y_lim2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_reverse1 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_reverse1 PARAMETER IN nextflow.config FILE:\n${y_reverse1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_reverse2 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_reverse2 PARAMETER IN nextflow.config FILE:\n${y_reverse2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_threshold1 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_threshold1 PARAMETER IN nextflow.config FILE:\n${y_threshold1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_threshold2 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_threshold2 PARAMETER IN nextflow.config FILE:\n${y_threshold2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_log1 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_log1 PARAMETER IN nextflow.config FILE:\n${y_log1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-if( ! y_log2 in String ){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_log2 PARAMETER IN nextflow.config FILE:\n${y_log2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
-}
-def file_exists5 = cute.exists()
-if( ! file_exists5){
- error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID cute_path PARAMETER IN nextflow.config FILE:\n${cute_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
-}
-
-// below : those variable are already used in the config file. Thus, to late to check them. And not possible to check inside the config file
-// system_exec
-// out_ini
-print("\n\nRESULT DIRECTORY: ${out_path}")
-print("\n\nWARNING: PARAMETERS ALREADY INTERPRETED IN THE .config FILE:")
-print(" system_exec: ${system_exec}")
-print(" out_path: ${out_path_ini}")
-print(" queue: ${queue}")
-print(" qos: ${qos}")
-print(" add_options: ${add_options}")
-print("\n\n")
-
-
-//////// end Checks
-
//////// Processes
-process WorkflowVersion { // create a file with the workflow version in out_path
- label 'bash' // see the withLabel: bash in the nextflow config file
- publishDir "${out}/reports", mode: 'copy'
+process workflowParam { // create a file with the workflow parameters in out_path
+ label 'bash'
+ publishDir "${out_path}/reports", mode: 'copy', overwrite: false
cache 'false'
+ input:
+ val modules
+
output:
- file "Run_info.txt"
+ path "Run_info.txt"
script:
"""
@@ -192,31 +40,31 @@ process WorkflowVersion { // create a file with the workflow version in out_path
echo "loaded modules (according to specification by the user thanks to the --modules argument of main.nf): ${modules}" >> Run_info.txt
fi
echo "Manifest's pipeline version: ${workflow.manifest.version}" >> Run_info.txt
- echo "result path: ${out}" >> Run_info.txt
+ echo "result path: ${out_path}" >> Run_info.txt
echo "nextflow version: ${nextflow.version}" >> Run_info.txt
echo -e "\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): ${launchDir}\\nprojectDir (directory where the main.nf script is located): ${projectDir}\\nworkDir (directory where tasks temporary files are created): ${workDir}" >> Run_info.txt
- echo -e "\\n\\nUSER VARIABLES:\\n\\nout_path: ${out}\\nsample_path: ${sample_path}" >> Run_info.txt
+ echo -e "\\n\\nUSER VARIABLES:\\n\\nout_path: ${out_path}\\nsample_path: ${sample_path}" >> Run_info.txt
"""
}
//${projectDir} nextflow variable
//${workflow.commandLine} nextflow variable
//${workflow.manifest.version} nextflow variable
-//Note that variables like ${out} are interpreted in the script block
+//Note that variables like ${out_path} are interpreted in the script block
process vcf_subfield_title {
label 'r_ext' // see the withLabel: bash in the nextflow config file
- publishDir "${out}/reports", mode: 'copy', pattern: "{*.txt}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+ publishDir "${out_path}/reports", mode: 'copy', pattern: "{*.txt}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
cache 'true'
input:
- file vcf from vcf_ch1
- file cute
+ path vcf // no parall
+ path cute
output:
- file "vcf_info_field_titles.txt" into vcf_info_field_titles_ch
- file "vcf_csq_subfield_titles.txt" into vcf_csq_subfield_titles_ch
- file "vcf_subfield_title_report.txt"
+ path "vcf_info_field_titles.txt", emit: vcf_info_field_titles_ch
+ path "vcf_csq_subfield_titles.txt", emit: vcf_csq_subfield_titles_ch
+ path "vcf_subfield_title_report.txt"
script:
"""
@@ -228,20 +76,20 @@ process vcf_subfield_title {
process fisher {
label 'python' // see the withLabel: bash in the nextflow config file
- publishDir "${out}/reports", mode: 'copy', pattern: "{fisher_report.txt}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+ publishDir "${out_path}/reports", mode: 'copy', pattern: "{fisher_report.txt}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
cache 'true'
input:
- tuple val(region2), file(vcf) from region_ch.combine(vcf_ch2) // parallelization expected for each value of region_ch
- file ped
- if(sample_path =~ /.*\.gz$/){file tbi}
- file vcf_info_field_titles from vcf_info_field_titles_ch.first()
- file vcf_csq_subfield_titles from vcf_csq_subfield_titles_ch.first()
+ tuple val(region2), path(vcf) // parallelization expected for each value of region_ch
+ path ped
+ path tbi
+ path vcf_info_field_titles
+ path vcf_csq_subfield_titles
val tsv_extra_fields
output:
- file "*.tsv" into fisher_ch1 // multi channel
- file "*.txt"
+ path "*.tsv", emit: fisher_ch1 // multi channel
+ path "*.txt"
script:
"""
@@ -255,19 +103,16 @@ process fisher {
"""
}
-fisher_ch1.collectFile(name: "fisher.tsv", skip:1, keepHeader:true).into{fisher_ch2 ; fisher_ch3 ; fisher_ch4 ; fisher_ch5}
-//fisher_ch2.subscribe{it -> it.copyTo("${out}")} // will be published below, after zipping
-
process miami_plot {
label 'r_ext' // see the withLabel: bash in the nextflow config file
- publishDir "${out}", mode: 'copy', pattern: "{*.png}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
- publishDir "${out}/reports", mode: 'copy', pattern: "{miami_report.txt}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+ publishDir "${out_path}", mode: 'copy', pattern: "{*.png}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+ publishDir "${out_path}/reports", mode: 'copy', pattern: "{miami_report.txt}", overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
cache 'true'
input:
- file fisher from fisher_ch3
- file chr
+ path fisher
+ path chr
val x_lim_val
val vgrid
val top_y_column
@@ -282,11 +127,11 @@ process miami_plot {
val y_threshold2
val y_log1
val y_log2
- file cute
+ path cute
output:
- file "*.png"
- file "miami_report.txt"
+ path "*.png"
+ path "miami_report.txt"
script:
"""
@@ -298,20 +143,20 @@ process miami_plot {
process tsv2vcf {
label 'bash' // see the withLabel: bash in the nextflow config file
- publishDir "${out}", mode: 'copy', overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+ publishDir "${out_path}", mode: 'copy', overwrite: false // https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
cache 'true'
input:
- file vcf from vcf_ch3
- file fisher from fisher_ch4
+ path vcf
+ path fisher
output:
- file "res_fisher.*"
+ path "res_fisher.*"
script:
"""
#!/bin/bash -ue
- PREHEADER='##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present'
+ PREHEADER='##fileformat=VCFv4.2;build by main.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present'
HEADER='#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO'
echo -e \$PREHEADER > res_fisher.vcf
FILENAME=\$(basename -- "${vcf}") # recover a file name without path
@@ -362,12 +207,11 @@ process tsv_compress {
//no channel input here for the vcf, because I do not transform it
input:
- file tsv from fisher_ch5
+ path tsv
// see the scope for the use of affected_patients which is already a variable from .config file
output:
- file "res_fisher.*"
-
+ path "res_fisher.*"
script:
"""
@@ -378,19 +222,19 @@ process tsv_compress {
}
-process Backup {
+process backup {
label 'bash' // see the withLabel: bash in the nextflow config file
- publishDir "${out}/reports", mode: 'copy', overwrite: false // since I am in mode copy, all the output files will be copied into the publishDir. See \\wsl$\Ubuntu-20.04\home\gael\work\aa\a0e9a739acae026fb205bc3fc21f9b
+ publishDir "${out_path}/reports", mode: 'copy', overwrite: false // since I am in mode copy, all the output files will be copied into the publishDir. See \\wsl$\Ubuntu-20.04\home\gael\work\aa\a0e9a739acae026fb205bc3fc21f9b
cache 'false'
input:
- file config_file
- file log_file
+ path config_file
+ path log_file
output:
- file "${config_file}" // warning message if we use file config_file
- file "${log_file}" // warning message if we use file log_file
- file "Log_info.txt"
+ path "${config_file}" // warning message if we use file config_file
+ path "${log_file}" // warning message if we use file log_file
+ path "Log_info.txt"
script:
"""
@@ -400,3 +244,235 @@ process Backup {
//////// end Processes
+
+
+//////// Workflow
+
+
+workflow {
+
+ //////// Options of nextflow run
+
+ print("\n\nINITIATION TIME: ${workflow.start}")
+
+ //////// end Options of nextflow run
+
+
+ //////// Options of nextflow run
+
+ // --modules (it is just for the process workflowParam)
+ params.modules = "" // if --module is used, this default value will be overridden
+ // end --modules (it is just for the process workflowParam)
+
+ //////// end Options of nextflow run
+
+
+ //////// Variables
+
+ modules = params.modules // remove the dot -> can be used in bash scripts
+ config_file = file("${projectDir}/nextflow.config") // file() create a path object necessary o then create the file
+ log_file = file("${launchDir}/.nextflow.log")
+
+ // from parameters (options of the nexflow command line)
+ modules = params.modules // remove the dot -> can be used in bash scripts
+ // end from parameters (options of the nexflow command line)
+
+
+ //////// end Variables
+
+
+ //////// Variables from config.file that need to be modified
+
+
+ if(x_lim == 'whole' || (x_lim == 'region' && region == 'none')){ // for the miami plot
+ x_lim_val = "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM" // I have added both notations "chr23", "chr24", "chr25" or "chrY", "chrX", "chrM" because either one or the other can be used in a VCF file
+ }else if(x_lim == 'region'){
+ x_lim_val = region
+ }else{
+ x_lim_val = x_lim // value for the miami plot
+ }
+
+ //////// end Variables from config.file that need to be modified
+
+
+ //////// Checks
+
+ if( ! (sample_path in String) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID sample_path PARAMETER IN repertoire_profiler.config FILE:\n${sample_path}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }else if( ! (file(sample_path).exists()) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID sample_path PARAMETER IN repertoire_profiler.config FILE (DOES NOT EXIST): ${sample_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+ }else if(sample_path =~ /.*\.gz$/){
+ if( ! (file("${sample_path}.tbi").exists()) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID .tbi FILE ASSOCIATED TO sample_path PARAMETER IN nextflow.config FILE: ${sample_path}.tbi\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\nOTHERWISE, USE tabix -p vcf <NAME>.vcf TO INDEX THE .gz FILE\n\n========\n\n"
+ }else{
+ tbi_file = file("${sample_path}.tbi")
+ }
+ }else{
+ tbi_file = file("NULL")
+ }
+ if( ! (ped_path in String) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ped_path PARAMETER IN repertoire_profiler.config FILE:\n${ped_path}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }else if( ! (file(ped_path).exists()) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID ped_path PARAMETER IN repertoire_profiler.config FILE (DOES NOT EXIST): ${ped_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+ }
+ if( ! (chr_path in String) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID chr_path PARAMETER IN repertoire_profiler.config FILE:\n${chr_path}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }else if( ! (file(chr_path).exists()) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID chr_path PARAMETER IN repertoire_profiler.config FILE (DOES NOT EXIST): ${chr_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+ }
+ if( ! region in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID region PARAMETER IN nextflow.config FILE:\n${region}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! tsv_extra_fields in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID tsv_extra_fields PARAMETER IN nextflow.config FILE:\n${tsv_extra_fields}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! x_lim in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID x_lim PARAMETER IN nextflow.config FILE:\n${x_lim}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! vgrid in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID vgrid PARAMETER IN nextflow.config FILE:\n${vgrid}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! top_y_column in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID top_y_column PARAMETER IN nextflow.config FILE:\n${top_y_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! bottom_y_column in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID bottom_y_column PARAMETER IN nextflow.config FILE:\n${bottom_y_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! color_column in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID color_column PARAMETER IN nextflow.config FILE:\n${color_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_lim1 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim1 PARAMETER IN nextflow.config FILE:\n${y_lim1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_lim2 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim2 PARAMETER IN nextflow.config FILE:\n${y_lim2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_reverse1 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_reverse1 PARAMETER IN nextflow.config FILE:\n${y_reverse1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_reverse2 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_reverse2 PARAMETER IN nextflow.config FILE:\n${y_reverse2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_threshold1 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_threshold1 PARAMETER IN nextflow.config FILE:\n${y_threshold1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_threshold2 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_threshold2 PARAMETER IN nextflow.config FILE:\n${y_threshold2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_log1 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_log1 PARAMETER IN nextflow.config FILE:\n${y_log1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! y_log2 in String ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_log2 PARAMETER IN nextflow.config FILE:\n${y_log2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }
+ if( ! (cute_path in String) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID cute_path PARAMETER IN repertoire_profiler.config FILE:\n${cute_path}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+ }else if( ! (file(cute_path).exists()) ){
+ error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID cute_path PARAMETER IN repertoire_profiler.config FILE (DOES NOT EXIST): ${cute_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
+ }
+
+ // below : those variable are already used in the config file. Thus, to late to check them. And not possible to check inside the config file
+ // system_exec
+ // out_ini
+ print("\n\nRESULT DIRECTORY: ${out_path}")
+ if("${system_exec}" != "local"){
+ print(" queue: ${queue}")
+ print(" qos: ${qos}")
+ print(" add_options: ${add_options}")
+ }
+ print("\n\n")
+
+
+ //////// end Checks
+
+ //////// Channels
+
+ vcf_ch = Channel.fromPath(sample_path)
+
+ if(region == 'none'){ // for combine below for parallelization of the fisher process
+ region_ch = Channel.from("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chr23", "chr24", "chr25", "chrY", "chrX", "chrM") // I have added both notations "chr23", "chr24", "chr25" or "chrY", "chrX", "chrM" because either one or the other can be used in a VCF file
+ }else{
+ if(region =~ /,/){
+ tempo = region.replaceAll(':.+,', ',')
+ }else{
+ tempo = region
+ }
+ tempo2 = tempo.replaceAll(':.+$', '')
+ tempo3 = tempo2.replaceAll(' ', '')
+ tempo4 = tempo3.split(",") // .split(",") split according to comma and create an array https://www.tutorialspoint.com/groovy/groovy_split.htm
+ region_ch = Channel.from(tempo4)
+ }
+
+
+ //////// end Channels
+
+
+ //////// files import
+
+ // in variable because a single file. If "NULL", will create a empty file, present in work folders, but that cannot be correctly linked. Thus, if the file has to be redirected into a channel inside a process, it will not work. Thus, in the first process using meta_file, I hard copy the NULL file if required (see below)
+ ped_file = file(ped_path) // in variable because a single file
+ chr_file = file(chr_path) // in variable because a single file
+ cute_file = file(cute_path) // in variable because a single file
+
+ //////// end files import
+
+
+
+ //////// Main
+
+ workflowParam(
+ modules
+ )
+
+ vcf_subfield_title(
+ vcf_ch,
+ cute_file
+ )
+
+ fisher(
+ region_ch.combine(vcf_ch),
+ ped_file,
+ tbi_file,
+ vcf_subfield_title.out.vcf_info_field_titles_ch.first(),
+ vcf_subfield_title.out.vcf_csq_subfield_titles_ch.first(),
+ tsv_extra_fields
+ )
+
+ fisher_ch2 = fisher.out.fisher_ch1.collectFile(name: "fisher.tsv", skip: 1, keepHeader: true)
+
+ miami_plot(
+ fisher_ch2,
+ chr_file,
+ x_lim_val,
+ vgrid,
+ top_y_column,
+ bottom_y_column,
+ color_column,
+ dot_border_color,
+ y_lim1,
+ y_lim2,
+ y_reverse1,
+ y_reverse2,
+ y_threshold1,
+ y_threshold2,
+ y_log1,
+ y_log2,
+ cute_file
+ )
+
+ tsv2vcf(
+ vcf_ch,
+ fisher_ch2
+ )
+
+ tsv_compress(
+ fisher_ch2
+ )
+
+ backup(
+ config_file,
+ log_file
+ )
+
+
+}
diff --git a/nextflow.config b/nextflow.config
index a1330690603252d275072396c9904d0e8d2715e5..e587a52f13d966defa22c7a130afd90f870d8853 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -172,19 +172,19 @@ process {
withLabel: bash {
container='gmillot/htslib_v1.0:gitlab_v9.1'
cpus=1 // only used when name = "local" in the executor part above
- memory='64G' // only used when name = "local" in the executor part above
+ memory='60G' // only used when name = "local" in the executor part above
}
withLabel: python {
container='gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7'
cpus=1 // only used when name = "local" in the executor part above
- memory='64G' // only used when name = "local" in the executor part above
+ memory='60G' // only used when name = "local" in the executor part above
}
withLabel: r_ext {
container='gmillot/r_v4.1.2_extended_v2.1:gitlab_v8.8'
cpus=1 // only used when name = "local" in the executor part above
- memory='64G' // only used when name = "local" in the executor part above
+ memory='60G' // only used when name = "local" in the executor part above
}
}