fix config channel

ghga-de · May 21, 2024 · 181d486 · 181d486
1 parent 46fc4d7
commit 181d486
Show file tree

Hide file tree

Showing 4 changed files with 5 additions and 3 deletions.
diff --git a/modules/local/get_contigs.nf b/modules/local/get_contigs.nf
@@ -38,7 +38,7 @@ process GET_CONTIGS {
             else
                 touch ALT_contigs.bed
             fi
-            if [-n "\$(samtools view -H $tumor | grep -P "SN:HLA")" ]; then
+            if [ -n "\$(samtools view -H $tumor | grep -P "SN:HLA")" ]; then
                 samtools view -H $tumor | grep -P "SN:HLA" | sed -e 's/@SQ\\tSN://' -e 's/\\tLN:/\\t0\\t/' -e 's/\\tAH.*//' | sort -V -k1,1 | cut -f 1 > HLA_contigs.bed
             else
                 touch HLA_contigs.bed

diff --git a/run_pipeline.sh b/run_pipeline.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 module load nextflow/22.07.1-edge
-nextflow run main.nf -profile dkfz_cluster_hg38,singularity --input assets/samplesheet_hg38_WGS.csv -resume
+nextflow run main.nf -profile dkfz_cluster_hg38,singularity --outdir results
diff --git a/testdata_hg37/samplesheet_test_37.csv b/testdata_hg37/samplesheet_test_37.csv
@@ -0,0 +1,2 @@
+sample,tumor,tumor_index,control,control_index
+test_withcontrol,testdata_hg37/tumor.bam,testdata_hg37/tumor.bam.bai,testdata_hg37/control.bam,testdata_hg37/control.bam.bai
diff --git a/workflows/snvcalling.nf b/workflows/snvcalling.nf
@@ -58,7 +58,7 @@ if (params.annotation_tool.contains("vep")){
 ref            = Channel.fromPath([params.fasta,params.fasta_fai], checkIfExists: true).collect()
 chr_prefix     = params.chr_prefix  ? Channel.value(params.chr_prefix) : Channel.value("")
 chrlength      = params.chrom_sizes ? Channel.fromPath(params.chrom_sizes, checkIfExists: true) : Channel.empty()   
-contigs        = params.contig_file ? Channel.fromPath(params.contig_file, checkIfExists: true) : Channel.empty()
+contigs        = params.contig_file ? Channel.fromPath(params.contig_file, checkIfExists: true) : Channel.value([[],[]])
 config         = Channel.fromPath("${projectDir}/assets/config/convertToStdVCF.json", checkIfExists: true).collect()
 
 // Annovar table folder