implement config of samples - csv over excel

ncherric · Jun 28, 2023 · 9dff45d · 9dff45d
1 parent c6ebdf5
commit 9dff45d
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Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/config/UserSampleTable.csv b/config/UserSampleTable.csv
@@ -0,0 +1,2 @@
+KPGP-00127  ftp://ftp.kobic.re.kr/pub/KPGP/2020_release_candidate/WGS_SR/KPGP-00127/KPGP-00127_L1_R1.fq.gz
+KPGP-00127  ftp://ftp.kobic.re.kr/pub/KPGP/2020_release_candidate/WGS_SR/KPGP-00127/KPGP-00127_L1_R2.fq.gz
diff --git a/config/config.yaml b/config/config.yaml
@@ -38,12 +38,12 @@ workdirPath: NEED PATH HERE
 
 # for downloading FastQ raw seq data make sure there is an Excel table or csv document with two columns and no header: Sample_Name,FTP_url
 # e.g KPGP-00127,ftp://ftp.kobic.re.kr/pub/KPGP/2020_release_candidate/WGS_SR/KPGP-00127/KPGP-00127_L1_R1.fq.gz
-samplesDict: config/UserSampleTable.xlsx
+samplesDict: config/UserSampleTable.csv
 # must include list of samples in one column with "sample" header, no matter if you use the download feature or if you re-direct ILIAD to FASTQ data path
 samples: config/samples.tsv
 
 # Same setup as above for if you are retrieving CRAM files from an FTP server
-cramSamplesDict: config/cramSampleTable.xlsx
+cramSamplesDict: config/cramSampleTable.csv
 cramSamples: config/cramSamples.tsv
 
 ###########################################################

diff --git a/config/cramSampleTable.csv b/config/cramSampleTable.csv
@@ -0,0 +1,2 @@
+NA12718 ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239480/NA12718.final.cram
+NA12718 ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239480/NA12718.final.cram.crai