fix tests

Author: priesgo

nextflow.config

@@ -15,8 +15,6 @@ profiles {
     params.prepare_bam_memory = "3g"
     params.mark_duplicates_cpus = 1
     params.mark_duplicates_memory = "3g"
-    params.skip_mark_duplicates_cpus = 1
-    params.skip_mark_duplicates_memory = "3g"
     params.realignment_around_indels_cpus = 1
     params.realignment_around_indels_memory = "3g"
     params.bqsr_cpus = 1

tests/test_01.sh

@@ -8,7 +8,6 @@ nextflow main.nf -profile test,conda --output $output
 test -s $output/sample1/sample1.preprocessed.bam || { echo "Missing output BAM file!"; exit 1; }
 test -s $output/sample1/sample1.preprocessed.bai || { echo "Missing output BAI file!"; exit 1; }
 test -s $output/sample1/software_versions.PREPARE_BAM.txt || { echo "Missing software versions file!"; exit 1; }
-test -s $output/sample1/software_versions.INDEX_BAM.txt || { echo "Missing software versions file!"; exit 1; }
 test -s $output/sample1/software_versions.MARK_DUPLICATES.txt || { echo "Missing software versions file!"; exit 1; }
 test -s $output/sample1/software_versions.HS_METRICS.txt || { echo "Missing software versions file!"; exit 1; }
 test -s $output/sample1/software_versions.METRICS.txt || { echo "Missing software versions file!"; exit 1; }