update help message

lifebit-ai · Dec 23, 2021 · d0aca44 · d0aca44
1 parent 1ad094b
commit d0aca44
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diff --git a/main.nf b/main.nf
@@ -42,6 +42,8 @@ def helpMessage() {
                                     false should be used to run local files on the HPC (Sumner).
                                     'TCGA' can also be used to download GDC data including HCMI data.
                                     (default: false)
+      --manifest                    Manifest file to download data from GTEX. (string)
+                                    (default: false)
       --key_file                    For downloading reads, use TCGA authentication token (TCGA) or dbGAP repository
                                     key (GTEx, path) or credentials.json file in case of 'GEN3-DRS'
                                     (default: false)

diff --git a/nextflow.config b/nextflow.config
@@ -11,6 +11,7 @@ params {
     rmats_pairs    = false
     run_name	     = false
     download_from  = false
+    manigest       = false
     sra_config_file= "${baseDir}/assets/sra-user-settings.mkfg"
     key_file       = false
     genome_fasta   = false