Closed zhouzhendiao closed 9 months ago
Hi @zhouzhendiao ! This is already possible with a user.config profile :) could you please create a config file such as the following :
process { withName:MAGECK_MLE { ext.args = '--control-sgrna "your-config-file" ' } }
and then in the command line specify -c user.config
let me know how it goes :) best, Laurence
Hi @LaurenceKuhl ,
I will try this later. Thanks for replying!
Hi i will close this issue, please feel free to re open if anything is unclear
Hi @LaurenceKuhl - my understanding is that these sorts of extra pipeline-specific parameters are best suited for the -params-file
rather than the -c config.yml
specification. Is it possible to implement something where we would specify the above as:
extra_mageck_mle_args: >-
--control-sgrna "gRNA_CONTROL_IDs.tsv"
or similar within a supplied -params-file
?
Note that when trying the above as
process {
withName: 'MAGECK_MLE' {
ext.args = '--control-sgrna "gRNA_annotated_geneSymbol_withID_CONTROLS.tsv" '
}
}
where my .tsv
contains a list of control gRNAs like
sgRNA56555
sgRNA56556
sgRNA56557
sgRNA56558
sgRNA56559
sgRNA56560
sgRNA56561
sgRNA56562
sgRNA56563
sgRNA56564
I get a FileNotFoundError
:
Caused by:
Process `NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE (treated_7hr_1,treated_7hr_2,treated_7hr_3_vs_control_1,control_2,control_3)` terminated with an error exit status (1)
Command executed:
mageck \
mle \
--control-sgrna "gRNA_annotated_geneSymbol_withID_CONTROLS.tsv" \
--threads 6 \
-k count_table.count.txt \
-n treated_7hr_1,treated_7hr_2,treated_7hr_3_vs_control_1,control_2,control_3 \
-d treated_7hr_1_treated_7hr_2_treated_7hr_3_vs_control_1_control_2_control_3.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE":
mageck: $(mageck -v)
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO @ Wed, 24 Jul 2024 12:58:58: Parameters: /usr/local/bin/mageck mle --control-sgrna gRNA_annotated_geneSymbol_withID_CONTROLS.tsv --threads 6 -k count_table.count.txt -n treated_7hr_1,treated_7hr_2,treated_7hr_3_vs_control_1,control_2,control_3 -d treated_7hr_1_treated_7hr_2_treated_7hr_3_vs_control_1_control_2_control_3.txt
INFO @ Wed, 24 Jul 2024 12:58:59: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Wed, 24 Jul 2024 12:58:59: Design matrix:
INFO @ Wed, 24 Jul 2024 12:58:59: [[1. 0.]
INFO @ Wed, 24 Jul 2024 12:58:59: [1. 0.]
INFO @ Wed, 24 Jul 2024 12:58:59: [1. 0.]
INFO @ Wed, 24 Jul 2024 12:58:59: [1. 1.]
INFO @ Wed, 24 Jul 2024 12:58:59: [1. 1.]
INFO @ Wed, 24 Jul 2024 12:58:59: [1. 1.]]
INFO @ Wed, 24 Jul 2024 12:58:59: Beta labels:baseline,treated_7hr_1_treated_7hr_2_treated_7hr_3_vs_control_1_control_2_control_3
INFO @ Wed, 24 Jul 2024 12:58:59: Included samples:control_1,control_2,control_3,treated_7hr_1,treated_7hr_2,treated_7hr_3
INFO @ Wed, 24 Jul 2024 12:59:00: Loaded samples:control_1;control_2;control_3;treated_7hr_1;treated_7hr_2;treated_7hr_3
INFO @ Wed, 24 Jul 2024 12:59:00: Sample index: 6;7;8;3;4;5
INFO @ Wed, 24 Jul 2024 12:59:00: Loaded 18899 genes.
Traceback (most recent call last):
File "/usr/local/bin/mageck", line 66, in <module>
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 83, in mageckmle_main
mageckcount_checkcontrolsgrna(args,sgrna2genelist)
File "/usr/local/lib/python3.9/site-packages/mageck/mageckCount.py", line 457, in mageckcount_checkcontrolsgrna
controlsglist=[line.strip() for line in open(args.control_sgrna)]
FileNotFoundError: [Errno 2] No such file or directory: 'gRNA_annotated_geneSymbol_withID_CONTROLS.tsv'
Description of feature
I have some non-target sgRNA in my library.
megeck count privide parameters
--control-sgrna
for generate the null distribution.Can you kindly add these paramter, thanks!