Update eQTLUtils container

eQTL-Catalogue · Nov 11, 2022 · 0aeb13f · 0aeb13f
1 parent 627b6df
commit 0aeb13f
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Showing 4 changed files with 14 additions and 14 deletions.
diff --git a/bin/normalisation/normaliseCountMatrix.R b/bin/normalisation/normaliseCountMatrix.R
@@ -47,7 +47,7 @@ if (FALSE) {
  opt$q="gene_counts"
  opt$o="."
  opt$t=NULL
- opt$keep_XY=TRUEz
+ opt$keep_XY=TRUE
  opt$filter_qc=TRUE
  opt$eqtlutils = "../eQTLUtils/"
 }

diff --git a/modules/normalisation.nf b/modules/normalisation.nf
@@ -5,7 +5,7 @@ process normalise_microarray{
  publishDir "${params.publishDir}/microarray", mode: 'copy'
 
  label 'process_medium'
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path count_matrix
@@ -41,7 +41,7 @@ process normalise_RNAseq_ge{
  publishDir "${params.publishDir}/ge", mode: 'copy', pattern: "qtl_group_median_tpms/*"
  publishDir "${params.publishDir}/", mode: 'copy', pattern: "*_tpm.tsv.gz" 
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path count_matrix
@@ -78,7 +78,7 @@ process normalise_RNAseq_ge{
 process normalise_RNAseq_exon{
  publishDir "${params.publishDir}/exon", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path count_matrix
@@ -113,7 +113,7 @@ process normalise_RNAseq_exon{
 process normalise_RNAseq_tx{
  publishDir "${params.publishDir}/tx", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path count_matrix
@@ -148,7 +148,7 @@ process normalise_RNAseq_tx{
 process normalise_RNAseq_txrev{
  publishDir "${params.publishDir}/txrev", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path count_matrix
@@ -184,7 +184,7 @@ process normalise_RNAseq_leafcutter{
  publishDir "${params.publishDir}/leafcutter", mode: 'copy'
 
  label 'process_medium'
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path count_matrix

diff --git a/modules/normalisation_multi.nf b/modules/normalisation_multi.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl=2
 process normalise_microarray{
  publishDir "${params.outdir}/$run_id/$study_name/normalised/microarray", mode: 'copy', pattern: "qtl_group_split_norm/*"
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  tuple val(run_id), val(study_name), file(quant_results_path), file(sample_metadata)
@@ -39,7 +39,7 @@ process normalise_RNAseq_ge{
  publishDir "${params.outdir}/$run_id/$study_name/normalised/ge", mode: 'copy', pattern: "qtl_group_median_tpms/*"
  publishDir "${params.outdir}/$run_id/$study_name/normalised/", mode: 'copy', pattern: "*_tpm.tsv.gz"
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  tuple val(run_id), val(study_name), file(quant_results_path), file(sample_metadata)
@@ -76,7 +76,7 @@ process normalise_RNAseq_ge{
 process normalise_RNAseq_exon{
  publishDir "${params.outdir}/$run_id/$study_name/normalised/exon", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  tuple val(run_id), val(study_name), file(quant_results_path), file(sample_metadata), file(tpm_quantile)
@@ -109,7 +109,7 @@ process normalise_RNAseq_exon{
 process normalise_RNAseq_tx{
  publishDir "${params.outdir}/$run_id/$study_name/normalised/tx", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  tuple val(run_id), val(study_name), file(quant_results_path), file(sample_metadata), file(tpm_quantile)
@@ -142,7 +142,7 @@ process normalise_RNAseq_tx{
 process normalise_RNAseq_txrev{
  publishDir "${params.outdir}/$run_id/$study_name/normalised/txrev", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  tuple val(run_id), val(study_name), file(quant_results_path), file(sample_metadata), file(tpm_quantile)
@@ -177,7 +177,7 @@ process normalise_RNAseq_leafcutter{
  publishDir "${params.outdir}/$run_id/$study_name/normalised/leafcutter", mode: 'copy'
 
  label 'process_medium'
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  tuple val(run_id), val(study_name), file(quant_results_path), file(sample_metadata), file(tpm_quantile)

diff --git a/modules/quality_control.nf b/modules/quality_control.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl=2
 process build_qc_report{
  publishDir "${params.outdir}/${params.study_name}/QC", mode: 'copy'
 
- container = 'quay.io/eqtlcatalogue/eqtlutils:v20.04.1'
+ container = 'quay.io/eqtlcatalogue/eqtlutils:v22.11.1'
 
  input:
  path script_path