correct something that was not an error while reading the input BAMs but it was close

Author: priesgo

README.md

@@ -76,22 +76,22 @@ Output:
 
 The table with VCF files expects two tab-separated columns without a header
 
-| Patient name          | VCF                                                             |
-|----------------------|------------------------------------------------------------------------|
-| patient_1             | /path/to/patient_1.vcf               |
-| patient_2             | /path/to/patient_2.vcf                    |
+| Patient name      | VCF                                    |
+|-------------------|----------------------------------------|
+| patient_1         | /path/to/patient_1.vcf                 |
+| patient_2         | /path/to/patient_2.vcf                 |
 
 The optional table with BAM files expects two tab-separated columns without a header.
 
-| Patient name          | Sample name:BAM                      |
-|----------------------|---------------------------------|
-| patient_1             | primary_tumor:/path/to/sample_1.primary.bam   |
-| patient_1             | metastasis_tumor:/path/to/sample_1.metastasis.bam   |
-| patient_1             | normal:/path/to/sample_1.normal.bam   |
-| patient_2             | primary_tumor:/path/to/sample_1.primary_1.bam   |
-| patient_2             | primary_tumor:/path/to/sample_1.primary_2.bam   |
-| patient_2             | metastasis_tumor:/path/to/sample_1.metastasis.bam   |
-| patient_2             | normal:/path/to/sample_1.normal.bam   |
+| Patient name       | Sample name:BAM                                   |
+|--------------------|---------------------------------------------------|
+| patient_1          | primary_tumor:/path/to/sample_1.primary.bam       |
+| patient_1          | metastasis_tumor:/path/to/sample_1.metastasis.bam |
+| patient_1          | normal:/path/to/sample_1.normal.bam               |
+| patient_2          | primary_tumor:/path/to/sample_1.primary_1.bam     |
+| patient_2          | primary_tumor:/path/to/sample_1.primary_2.bam     |
+| patient_2          | metastasis_tumor:/path/to/sample_1.metastasis.bam |
+| patient_2          | normal:/path/to/sample_1.normal.bam               |
 
 Each patient can have any number of samples. Any sample can have any number of BAM files, annotations from the 
 different BAM files of the same sample will be provided with suffixes _1, _2, etc.

main.nf

@@ -58,8 +58,8 @@ else if (params.input_vcf) {
 if (params.input_bams) {
     Channel
     .fromPath(params.input_bams)
-    .splitCsv(header: ['name', 'sample_name', 'bam'], sep: "\t")
-    .map{ row-> tuple(row.name, row.sample_name, row.bam) }
+    .splitCsv(header: ['name', 'bam'], sep: "\t")
+    .map{ row-> tuple(row.name, row.bam) }
     .set { input_bams }
 }