Comments (3)
The --ignore
option seems to solve the problem!
I close this!!
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Hi @MostafaYA ,
No problems mate - thankfully this was suggested by Alex Weisberg.
A bit of a self plug, but I'd also give Hybracter https://github.com/gbouras13/hybracter a try as it should handle these cases for you automatically (I'd love some feedback!) :)
I also know Dnaapler will probably soon be in Dragonflye https://github.com/rpetit3/dragonflye - so that would be another good option to try. Just tagging you in here too @rpetit3 I'm not sure how you have handled non-circularised contigs but this concern is something to think about if you haven't thought of it!
George
from dnaapler.
Hi, thanks for the great pipelines.
Below is my code to auto-ignore the non-circular contigs
rule noncircular_contigs:
input:
rules.copy_flye_data.output[1],
output:
results_per_sample_dir + "{sample}/4_genome_rotation/noncircular_contigs.tsv",
conda:
envs_folder + "csvtk.yaml"
shell:
"""
csvtk filter2 -t -C $ -f '$4== "N" ' {input} -o {output}
"""
rule rotate_genome:
input:
rotate_genome_input(),
rules.noncircular_contigs.output[0],
output:
dir = temp(directory(results_per_sample_dir + "{sample}/tmp_rotation")),
contigs= results_per_sample_dir + "{sample}/4_genome_rotation/{sample}.fasta",
summary= results_per_sample_dir + "{sample}/4_genome_rotation/{sample}.reorientation_summary.tsv"
threads: 16
conda:
envs_folder + "dnaapler.yaml"
log: results_per_sample_dir + "{sample}/4_genome_rotation/dnaapler.log"
params:
options = "--force "
shell:
"""
dnaapler all {params.options} \
--prefix {wildcards.sample} \
--output {output.dir} \
--threads {threads} \
--ignore {input[1]} \
--input {input[0]} 2>&1 | tee {log} >/dev/null
cp {output.dir}/{wildcards.sample}_reoriented.fasta {output.contigs}
cp {output.dir}/{wildcards.sample}_all_reorientation_summary.tsv {output.summary}
"""
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Related Issues (20)
- fix start at pat gene instead of dnaA HOT 5
- add ignore option as well as all databases option HOT 12
- Error with dnaapler all on bacterial chromosome and plasmids HOT 3
- [Question] Do reoriented contigs match the strandedness of the balst result? HOT 4
- Improve autocomplete HOT 4
- [JOSS Review] - Text corrections and suggestions HOT 3
- [JOSS Review] - Documentation HOT 4
- [JOSS Review] Typos in CONTRIBUTING.md HOT 2
- [JOSS Review] Authorship list HOT 2
- [JOSS Review] Installation instructions in the readthedocs HOT 2
- [JOSS Review] Clarifying the fallback behaviour from BLAST to pyrodigal HOT 8
- Option to specify start gene type in all mode HOT 3
- Add option to annotate fasta headers with Gene_Reoriented HOT 2
- min and max length criteria HOT 1
- dnaapler all --autocomplete not running HOT 4
- Add archaea support HOT 7
- Option to ignore errors linked to genome HOT 7
- Error with subset of samples in pipeline HOT 1
- Support reorientation of as many contigs as possible
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