Individual steps are not working.

[araboapresyan]

Describe the bug I tried to run multi_rna with individual steps but it works only for "sample" and "all" arguments.

run.sh multi_rna\ --mapfile ./my.mapfile\ --genomeDir /media/arabo/DATA/genomes/xenopus_tropicalis/ncbi_UCB_Xtro_10.0/celescope_genome\ --thread 8\ --mod shell\ --steps_run barcode

Result $sh run.sh 2024-04-10 17:57:39,260 - celescope.tools.multi.parse_mapfile - INFO - start... 2024-04-10 17:57:39,267 - celescope.tools.multi.parse_mapfile - INFO - done. time used: 0:00:00.007206 Traceback (most recent call last): File "/home/arabo/anaconda3/envs/celescope/bin/multi_rna", line 8, in sys.exit(main()) File "/home/arabo/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/rna/multi_rna.py", line 40, in main multi.run() File "/home/arabo/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/multi.py", line 421, in run self.run_steps() File "/home/arabo/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/multi.py", line 382, in run_steps method_to_call(sample) File "/home/arabo/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/multi.py", line 284, in barcode cmd_line = self.get_cmd_line(step, sample) File "/home/arabo/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/multi.py", line 248, in get_cmd_line f'--outdir {self.outdir_dic[sample][step]} ' KeyError: 'barcode'

Version 2.0.7

[zhouyiqi91]

In celescope v2, there is no barcode step in multi_rna. Available steps are sample,starsolo,analysis. https://github.com/singleron-RD/CeleScope/blob/master/celescope/rna/__init__.py

[araboapresyan]

Thanks. Then, is there any way to perform only barcoding step with V2, or to get intermediate fastq files?

[zhouyiqi91]

you can use the barcode step from other pipeline, for example,  celescope vdj barcode

----------Reply to Message---------- On Thu, Apr 11, 2024 18:26 PM @.***> wrote:

Thanks. Then, is there any way to perform only barcoding step with V2, or to get intermediate fastq files?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[araboapresyan]

Thanks.Works for me.