update indent and comment

nf-core · Jan 29, 2024 · fe0ab74 · fe0ab74
1 parent 09999ba
commit fe0ab74
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -27,7 +27,7 @@ params {
 
     //Germlinecnvcaller options
     gcnv_scatter_content = 2
-    gcnv_ploidy_priors     = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
+    gcnv_ploidy_priors   = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
 
     // Small reference genome
     genome            = null

diff --git a/nextflow.config b/nextflow.config
@@ -28,7 +28,7 @@ params {
     gcnv_scatter_content        = 5000
     gcnv_segmental_duplications = null
 
-    // Germlinecnvcaller options
+    // Gens options
     gens_bin_length             = 100
 
     // CNVkit options

diff --git a/subworkflows/local/gens_pon.nf b/subworkflows/local/gens_pon.nf
@@ -1,9 +1,9 @@
 include { GATK4_COLLECTREADCOUNTS             } from '../../modules/nf-core/gatk4/collectreadcounts/main'
+include { GATK4_CREATEREADCOUNTPANELOFNORMALS } from '../../modules/nf-core/gatk4/createreadcountpanelofnormals/main'
 include { GATK4_PREPROCESSINTERVALS           } from '../../modules/nf-core/gatk4/preprocessintervals/main'
 include { PICARD_CREATESEQUENCEDICTIONARY     } from '../../modules/nf-core/picard/createsequencedictionary/main'
 include { SAMTOOLS_FAIDX                      } from '../../modules/nf-core/samtools/faidx/main'
 include { SAMTOOLS_INDEX                      } from '../../modules/nf-core/samtools/index/main'
-include { GATK4_CREATEREADCOUNTPANELOFNORMALS } from '../../modules/nf-core/gatk4/createreadcountpanelofnormals/main'
 
 workflow GENS_PON {
     take:
@@ -80,12 +80,12 @@ workflow GENS_PON {
 
         GATK4_CREATEREADCOUNTPANELOFNORMALS (ch_readcounts_out)
 
-        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
-        ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
-        ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
-        ch_versions = ch_versions.mix(GATK4_PREPROCESSINTERVALS.out.versions)
         ch_versions = ch_versions.mix(GATK4_COLLECTREADCOUNTS.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_CREATEREADCOUNTPANELOFNORMALS.out.versions.first())
+        ch_versions = ch_versions.mix(GATK4_PREPROCESSINTERVALS.out.versions)
+        ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
+        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+        ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
     emit:
         genspon     = GATK4_CREATEREADCOUNTPANELOFNORMALS.out.pon