update documentation

TRON-Bioinformatics · May 6, 2021 · dc4672d · dc4672d
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diff --git a/README.md b/README.md
@@ -66,9 +66,6 @@ Optional input:
     * --dbsnp: path to the dbSNP VCF (required to perform BQSR)
     * --known_indels1: path to a VCF of known indels (optional to perform realignment around indels)
     * --known_indels2: path to a second VCF of known indels (optional to perform realignment around indels)
-    **NOTE**: if any of the reference parameters is not provided, default hg19 resources under
-    /projects/data/gatk_bundle/hg19/ will be used
-
     * --intervals: path to an intervals file to collect HS metrics from, this can be built with Picard's BedToIntervalList (default: None)
     * --hs_metrics_target_coverage: name of output file for target HS metrics (default: None)
     * --hs_metrics_per_base_coverage: name of output file for per base HS metrics (default: None)

diff --git a/nextflow.config b/nextflow.config
@@ -89,9 +89,6 @@ Optional input:
     * --dbsnp: path to the dbSNP VCF (required to perform BQSR)
     * --known_indels1: path to a VCF of known indels (optional to perform realignment around indels)
     * --known_indels2: path to a second VCF of known indels (optional to perform realignment around indels)
-    **NOTE**: if any of the reference parameters is not provided, default hg19 resources under
-    /projects/data/gatk_bundle/hg19/ will be used
-
     * --intervals: path to an intervals file to collect HS metrics from, this can be built with Picard's BedToIntervalList (default: None)
     * --hs_metrics_target_coverage: name of output file for target HS metrics (default: None)
     * --hs_metrics_per_base_coverage: name of output file for per base HS metrics (default: None)