Closed s-junguy closed 5 months ago
rhysnewell
commented
6 months ago Hello,
Thanks for pointing out the formatting error in the example tsv, I'll fix that up. It should be tabs not spaces in that final column.
Would you please be able to past an example of the csv/tsv file you've been using?
What is your reason for using an older version of aviary? Have you tried with a newer version? I'd highly recommend updating to the latest version
rhysnewell
commented
6 months ago I have managed to reproduce this is issue and working on a fix. For now, you can add --write-script aviary_script.sh to your command and it should write all the batch commands to single file which you can then run as a bash script. This should perform the same functions as if running all within aviary
s-junguy
commented
6 months ago Thanks for your help! This is my samples.csv:
sample,short_reads_1,short_reads_2,long_reads,long_read_type,assembly,coassemble
P19752-101,/home/user/all_fastq/P19752_101_S33_L002_R1_001.fastq.gz,/home/user/all_fastq/P19752_101_S33_L002_R2_001.fastq.gz,NA,NA,NA,False
P19752-102,/home/user/all_fastq/P19752_102_S34_L002_R1_001.fastq.gz,/home/user/all_fastq/P19752_102_S34_L002_R2_001.fastq.gz,NA,NA,NA,False
P19752-103,/home/user/all_fastq/P19752_103_S35_L002_R1_001.fastq.gz,/home/user/all_fastq/P19752_103_S35_L002_R2_001.fastq.gz,NA,NA,NA,False
P19752-104,/home/user/all_fastq/P19752_104_S36_L002_R1_001.fastq.gz,/home/user/all_fastq/P19752_104_S36_L002_R2_001.fastq.gz,NA,NA,NA,False
P19752-105,/home/user/all_fastq/P19752_105_S37_L002_R1_001.fastq.gz,/home/user/all_fastq/P19752_105_S37_L002_R2_001.fastq.gz,NA,NA,NA,False
P19752-106,/home/user/all_fastq/P19752_106_S38_L002_R1_001.fastq.gz,/home/user/all_fastq/P19752_106_S38_L002_R2_001.fastq.gz,NA,NA,NA,False
When I was working with the Aviary pipeline, there was only the version 0.8.0 available. I have just created the issue now and then I saw that you have a newer version available so there is no specific reason why I worked with the older version.
rhysnewell
commented
5 months ago Did using the --write-script flag fix your issue here?
s-junguy
commented
5 months ago Yes, it did. Thank you!
Hi, I want to run aviary with a batch file and tried it with a .tsv and then with a .csv file. In your example .tsv file, the last 2 columns are not separated by but by 2 spaces. I tried to run aviary with a .tsv file that contains columns just separated by and I also tried it with a .tsv file, where the last 2 columns were separated by 2 spaces but none of those options worked. Submitting a .csv file also did not work.
So, how can I run the complete workflow of aviary with a batch file?
If I submit a .csv file, it only creates a config file.
output file:
I use Illumina paired end libraries (10 GB per library). I still use the the old aviary version 0.8.0.