update replication

replication/gwascat/README.md

@@ -16,8 +16,8 @@ script using gwas catalog to compared gwas summary statistics to compared gwas s
   * `head_A1` ["ALLELE1"]
   * `head_A0` ["ALLELE0"]
  *  gwas catalog : algorithm download version of gwas catalog from ucsc, separate by comma
-  * `pheno` : un phenotype
-  * `file_pheno` : file containing list of phenotype extracted from gwas catalog
+  * `pheno_gc` : phenotype from gwas catalog
+  * `file_pheno_gc` : file containing list of phenotype extracted from gwas catalog
   * `list_chro` : list chro to analyse, separate by x-y (x to y) and comma [1-22]
  * `clump_r2` : min pvalue used for clump and ld 
  * `size_win_kb` : size in kb to analyse used in clump, ld and windows analyse
@@ -28,11 +28,11 @@ script using gwas catalog to compared gwas summary statistics to compared gwas s
 ### list of phenotypes available
 to obtain list of phenotype without run algorinm
 """
-nextflow run h3abionet/h3agwas/replication/gwascat/main.nf --justpheno 1 --output_dir gwascatpheno/ --output gwascatpheno -resume -profile slurm
+nextflow run h3abionet/h3agwas/replication/gwascat/main.nf --justpheno_gc 1 --output_dir gwascatpheno/ --output gwascatpheno -resume -profile slurm
 """
 
 ### GWAS catalog :
-extract from gwas catalog postiion and chromosome relative to `file_pheno` or `pheno` and `list_chro`. computed heritabilite, beta and se for input
+extract from gwas catalog postiion and chromosome relative to `file_pheno_gc` or `pheno_gc` and `list_chro`. computed heritabilite, beta and se for input
 OR transformed using log2 and defined if column contains information higher than 1
 
 
@@ -101,24 +101,21 @@ z values defined as beta / se
 
 ### process 
 
- * process dl\_gwascat\_hg19 : optional if gwascat is not give as parameter
- * process formatgwascat\_pheno : format gwas catalog, if just\_pheno
- * process   formatgwascat : format gwast catalog
- * process extractgwas\_fromgwascat : extract position from gwas present in positoins of gwas catalog 
+* process dl\_gwascat\_hg19 : optional if gwascat is not give as parameter
+* process formatgwascat\_pheno : format gwas catalog, if just\_pheno
+* process   formatgwascat : format gwast catalog
+* process extractgwas\_fromgwascat : extract position from gwas present in positoins of gwas catalog 
   * file description 
   * sub\_plk : sub plink, extracted positions from 1) gwas 2)gwas catalog
-process update_rs{
-process clump_aroundgwascat{
-process computedstat_pos{
-process  computedstat_windneutre{
-process computedstat_win{
-process computed_ld{
-process computed_ld_stat{
-process computed_clump_stat{
-process build_ldwind{
-process computed_ld2_stat{
-process computed_ldext_stat{
- process computed_ldwind_stat{
-process computed_ldwindext_stat{
+* process update\_rs : process to format plink file with specifi rs
+* process clump\_aroundgwascat : clump around each gwas cat 
+* process computedstat\_pos : exraction of position from gwas catalog on summary statistics 
+* process  computedstat\_windneutre : 
+* process computedstat\_win : computed statistcs by windows
+* process computed\_ld :extraction of positions from gwas catalog and summary statistics in LD
+* process computed\_ld\_stat :  computed statistics from ` computed\_ld`
+* process computed\_clump\_stat : computed statistics using clump function from plink
+* process build\_ldwind
+* process computed\_ldwind\_stat
 
 

replication/gwascat/main.nf

@@ -151,7 +151,7 @@ params.gwascat_format="USCS"
 
 params.gwas_cat_ftp="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/gwasCatalog.txt.gz"
 
-params.file_pheno=""
+params.file_pheno_gc=""
 params.list_chro="1-22"
 
 
@@ -239,17 +239,17 @@ System.exit(-1)
 }
 
 listchro=getlistchro(params.list_chro)
-if(params.file_pheno!=''){
-file_pheno_ch=file(params.file_pheno, checkIfExists:true)
+if(params.file_pheno_gc!=''){
+file_pheno_gc_ch=file(params.file_pheno_gc, checkIfExists:true)
 }else{
-file_pheno_ch=file('nofile')
+file_pheno_gc_ch=file('nofile')
 }
 process formatgwascat{
    label 'R'
    publishDir "${params.output_dir}/gwascat",  mode:'copy'
    input :
       file(gwascat) from gwascat_init_ch
-      file(filepheno) from file_pheno_ch
+      file(filepheno) from file_pheno_gc_ch
    output :
        file("${out}_range.bed") into gwascat_rangebed
        file("${out}.pos") into (gwascat_pos_subplk, gwascat_pos_ld2, gwascat_pos, gwascat_poswindneutre)
@@ -259,7 +259,7 @@ process formatgwascat{
    script :
      chroparam= (params.list_chro=='') ? "" : " --chro ${listchro.join(',')}"
      phenoparam= (params.pheno_gc=='') ? "" : " --pheno \"${params.pheno_gc}\" "
-     phenoparam= (params.file_pheno=='') ? " $phenoparam " : " --file_pheno $filepheno "
+     phenoparam= (params.file_pheno_gc=='') ? " $phenoparam " : " --file_pheno_gc $filepheno "
      out=params.output+'_gwascat'
    """
    format_gwascat.r --file $gwascat $chroparam $phenoparam --out $out --wind ${params.size_win_kb}  --chro_head ${params.head_chro_gwascat} --bp_head ${params.head_bp_gwascat} --pheno_head ${params.head_pheno_gwascat} --beta_head ${params.head_beta_gwascat} --ci_head ${params.head_ci_gwascat} --p_head ${params.head_pval_gwascat}  --n_head ${params.head_n_gwascat} --freq_head ${params.head_af_gwascat} --rs_head ${params.head_rs_gwascat} --riskall_head ${params.head_riskall_gwascat} --format $format