How can I fix config file when I only have DNA data?

[Donbbit]

Hi, I used Scanneo2 when I only have dna_normal and dna_tumor data, I changed the config like this:

Reference

General settings

reference:
release: 111
nonchr: false
threads: 30
mapq: 30 # overall required mapping quality
basequal: 20 # overall required base quality

data:
name: D1
dnaseq:
dna_normal: /hsfscqjf3/DIPSEQ/zfssz8/CNGB_DATA/BGISEQ01/DIPSEQ/DIPSEQT20/P24Z10200N0995_Temp/DT2411609481-1/250210_SEQ081_FP500002421_L01_SP2501130808/FP500002421_L01_375_1.fq.gz /hsfscqjf3/DIPSEQ/zfssz8/CNGB_DATA/BGISEQ01/DIPSEQ/DIPSEQT20/P24Z10200N0995_Temp/DT2411609481-1/250210_SEQ081_FP500002421_L01_SP2501130808/FP500002421_L01_375_2.fq.gz
dna_tumor1: /hsfscqjf3/DIPSEQ/zfssz8/CNGB_DATA/BGISEQ01/DIPSEQ/DIPSEQT20/P24Z10200N0995_Temp/D2411320266/250210_SEQ082_FP500002422_L01_SP2501130799/FP500002422_L01_492_1.fq.gz /hsfscqjf3/DIPSEQ/zfssz8/CNGB_DATA/BGISEQ01/DIPSEQ/DIPSEQT20/P24Z10200N0995_Temp/D2411320266/250210_SEQ082_FP500002422_L01_SP2501130799/FP500002422_L01_492_2.fq.gz
dna_tumor2: /hsfscqjf3/DIPSEQ/zfssz8/CNGB_DATA/BGISEQ01/DIPSEQ/DIPSEQT20/P24Z10200N0995_Temp/D2411320262/250210_SEQ082_FP500002422_L01_SP2501130795/FP500002422_L01_488_1.fq.gz /hsfscqjf3/DIPSEQ/zfssz8/CNGB_DATA/BGISEQ01/DIPSEQ/DIPSEQT20/P24Z10200N0995_Temp/D2411320262/250210_SEQ082_FP500002422_L01_SP2501130795/FP500002422_L01_488_2.fq.gz
rnaseq:
rna_tumor:
normal: dna_normal

custom:
variants:
hlatyping:
MHC-I:
MHC-II:

pre-processing (only applied on fastq reads)

preproc:
activate: true # whether (=true) or not (=false) to include pre-processing
minlen: 10
slidingwindow:
activate: true
wsize: 3
wqual: 20

alingment

align:
chimSegmentMin: 20
chimScoreMin: 10
chimJunctionOverhangMin: 10
chimScoreDropMax: 30
chimScoreSeparation: 10

variant calling

alternative splicing

altsplicing:
activate: true # whether (=true) or not (=false) to include alternative splicing events
confidence: 3 # confidence level (1,2 or 3) - filtering of input alignments
iterations: 5 # number of iteratios (when adding intro edges) - increases sensitivity
edgelimit: 250 # limit max number of edges in graph - affects the runtime

exitron splicing

exitronsplicing:
activate: true # whether (=true) or not (=false) to include exitron-splicing events
ao: 3 # allele observation
pso: 0.05 # percent spliced out
#strand: 1 # strand specificity of library (0=unstranded, 1=forward, 2=reverse)
strand: XS # strand specificity of library (0=XS, 1=RF, 2=FR)

gene fusion

genefusion:
activate: true # whether (=true) or not (=false) to include gene fusion events
maxevalue: 0.3
suppreads: 2 # all fusions with less than suppreads are discarded
maxsuppreads: 1000
maxidentity: 0.3 # genes with fraction of identity are discarded (homologs)
hpolymerlen: 6 # removes breakpoints adjacent to homopolymers of length
readthroughdist: 10000 # distance between breakpoints with less than distance
minanchorlen: 20 # removes fusions whose segments are less than minchimlen
splicedevents: 4 # fusions between genes need at least this many spliced breakpoints
maxkmer: 0.6 # remove reads with repetitive 3-mer that make up more than maxkmer
fraglen: 200 # mean fragment length
maxmismatch: 0.01

indel

indel:
activate: true # whether (=true) or not (=false) to include indels
type: all # long, short, all
mode: DNA # DNA, RNA or BOTH -

strategy for optimizing posterior probability threshold

strategy: OPTIMAL_F_SCORE # OPTIMAL_F_SCORE, FALSE_DISCOVERY_RATE, CONSTANT
fscorebeta: 1.0 # rel. weight of recall to precision (when OPTIMAL_F_SCORE is selected)
fdr: 0.05 # false discovery rate (when FALSE_DISCOVERY_RATE is selected)
sliplen: 8 # min number of reference bases to suspect slippage event
sliprate: 0.1 # frequency of slippage when it is supsected

quantification:
mode: DNA # RNA, RNA or BOTH

hlatyping:
class: BOTH # I, II or BOTH

specific path for class II hlatyping (only required when class: II, or BOTH)

MHC-I_mode: DNA # DNA, RNA, or custom (if empty alleles have to be specified in custom)
MHC-II_mode: DNA # DNA, RNA, or custom (if empty alleles have to be specified in custom)

specific path for class II hlatyping (only required when class: II, or BOTH)

freqdata: /hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/soft/hlahd.1.7.0/freq_data/
split: /hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/soft/hlahd.1.7.0/HLA_gene.split.txt
dict: /hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/soft/hlahd.1.7.0/dictionary/

prioritization:
class: I # I, II or BOTH
lengths:
MHC-I: 8,9,10,11
MHC-II: 13,14,15

And I got the error :
Config file /hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/Project/1.ESCA/1.scanneo2/D1/config.yaml is extended by additional config specified via the command line.
Traceback (most recent call last):
File "/hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/lib/python3.12/site-packages/snakemake/cli.py", line 1898, in args_to_api
dag_api = workflow_api.dag(
^^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
return DAGApi(
^^^^^^^
File "", line 6, in init
File "/hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/lib/python3.12/site-packages/snakemake/api.py", line 436, in post_init
self.workflow_api._workflow.dag_settings = self.dag_settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/lib/python3.12/site-packages/snakemake/api.py", line 383, in _workflow
workflow.include(
File "/hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/lib/python3.12/site-packages/snakemake/workflow.py", line 1382, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/Project/1.ESCA/1.scanneo2/D1/workflow/Snakefile", line 27, in
include: "rules/custom.smk"
File "/hsfscqjf1/ST_CQ/P23Z32300N0005/lvmeiqi/software/miniconda3/envs/scanneo2/lib/python3.12/site-packages/snakemake/workflow.py", line 1382, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/Project/1.ESCA/1.scanneo2/D1/workflow/rules/common.smk", line 126, in
config['data'] = data_structure(config['data'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/Project/1.ESCA/1.scanneo2/D1/workflow/rules/common.smk", line 11, in data_structure
config['data']['rnaseq'], filetype, readtype = handle_seqfiles(config['data']['rnaseq'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/Project/1.ESCA/1.scanneo2/D1/workflow/rules/common.smk", line 64, in handle_seqfiles
return mod_seqdata, filetype[0], readtype[0]
^^^^^^^^^^^^^^
IndexError: list index out of range

What should I do when I don't have rna data?

[riasc]

Hello,

thanks for your issue. So basically you have to leave rnaseq empty. Meaning:

rnaseq:
normal: dna_normal

Just remove rnatumor. Then this should work. Currently working on an update that exits this more gracefully.
Thanks

[Donbbit]

Hello, 你好,

thanks for your issue. So basically you have to leave rnaseq empty. Meaning:谢谢你的问题。所以基本上你要让rnaseq为空。意义:

rnaseq:
normal: dna_normal

Just remove rnatumor. Then this should work. Currently working on an update that exits this more gracefully. Thanks 谢谢只要移开。这样就可以了。目前正在进行更新，退出这个更优雅。

Thanks for your reply! And I changed the config like:

rnaseq:
normal: dna_normal

And when I test the pipeline I got this:
snakemake --dag | dot -Tpdf > pipe.pdf

Building DAG of jobs...
Error: : syntax error in line 1 near 'rnaseq'