added default -doMajorMinor 1 to output angsd beagle format

CHANGELOG.md

@@ -9,18 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
-- [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination`
-- [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
-- Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
-- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
-- [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty
-- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data.  `
-- [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file.
-- [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
-- [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex.
-- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails.
-- [672](https://github.com/nf-core/eager/issues/672) - Removed java parameter from picard tools which could cause memory issues
-- [679](https://github.com/nf-core/eager/issues/679) - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
+- [#690](https://github.com/nf-core/eager/pull/690) - Fixed ANGSD output mode for beagle by setting `-doMajorMinor 1` as default in that case
 
 ### `Dependencies`
 

main.nf

@@ -463,7 +463,7 @@ if (params.run_genotyping){
   }
 
   if (params.genotyping_tool == 'angsd' && ! ( params.angsd_glformat == 'text' || params.angsd_glformat == 'binary' || params.angsd_glformat == 'binary_three' || params.angsd_glformat == 'beagle' ) ) {
-    exit 1, "[nf-core/eager] error: please check your ANGSD genotyping model! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glmodel '${params.angsd_glmodel}'."
+    exit 1, "[nf-core/eager] error: please check your ANGSD output format! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glformat '${params.angsd_glformat}'."
   }
 
   if ( !params.angsd_createfasta && params.angsd_fastamethod != 'random' ) {
@@ -2836,10 +2836,11 @@ process genotyping_angsd {
   }
 
   def angsd_fasta = !params.angsd_createfasta ? '' : params.angsd_fastamethod == 'random' ? '-doFasta 1 -doCounts 1' : '-doFasta 2 -doCounts 1' 
+  def angsd_majorminor = params.angsd_glformat != "beagle" ? '' : '-doMajorMinor 1'
   """
   echo ${bam} > bam.filelist
   mkdir angsd
-  angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_fasta} -out ${samplename}.angsd
+  angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_majorminor} ${angsd_fasta} -out ${samplename}.angsd
   """
 }