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Hello! I would like to manually edit certain pipel...
# sarek
l
Hello! I would like to manually edit certain pipeline parameters, overriding the default settings. Is there a simple way to disable selected parameter validation tests? For example, I would like to provide 
--known-sites
manually within the 
baserecalibrator
module, and avoid messages like: 
Base quality score recalibration requires at least one resource file. Please provide at least one of
--dbsnp` or 
--known_indels
Any tips and hints welcome:)
r
Would providing it via the run command not work: 
nextflow run ... --known_sites my-known-sites.vcf.gz  --known_sites_tbi my-known-sites.vcf.gz.tbi
? and set 
dbsnp
and so to false
l
No, unfortunately this produces this warning: 
WARN: The following invalid input values have been detected:
* --known_sites: /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz
* --known_sites_tbi: /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi
r
can you share the command you used please
l
I also try providing it via 
--known-snps
but same issue occured. By the way, I find it a bit confusing (maybe other users may as well) that 
--known_indels
and `--known_snps`are separate parameters. Wouldn't a single 
--known_sites
parameter accepting multiple vcf files be much more intuitive? Maybe I'm missing something here, but I still trying to figure how to override the validation, and configure the command module by manually providing these files.
command:
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nextflow run /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sarek \
    -profile pdc_kth \
    -name $1 \
    -params-file /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/$2 \
    --project=${COMPUTE_ACCOUNT} \
    --email=${USER_E_MAIL} \
    --step prepare_recalibration \
    --known_snps /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz \
    --known_snps_tbi /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi
json:
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{
  "input": "/cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sample_tables/atac_bams_for_sarek_1samp.csv",
  "outdir": "/cfs/klemming/projects/supr/sllstore2017078/lech/sarek/ail_recal_test1",
  "genome": "",
  "no_intervals": false,
  "tools": "deepvariant,freebayes,strelka,haplotypecaller",
  "concatenate_vcfs": true,
  "joint_germline": true,
  "save_output_as_bam": true,
  "known_indels_vqsr": false,
  "known_snps_vqsr": false,
  "ngscheckmate_bed": false,
  "use_gatk_spark": "baserecalibrator",
  "fasta": "/cfs/klemming/projects/snic/sllstore2017078/lech/sarek/refs/112/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna_sm.toplevel.fa",
  "igenomes_ignore": true
}
r
It's because for some of the haplotypecaller path we need to differentiate with also giving these filters https://github.com/nf-core/sarek/blob/e92242ead3dff8e24e13adbbd81bfbc0b6862e4c/conf/igenomes.config#L33 to make sure the right files end up with the right filters we had to pslit the parameter
just to confirm
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nextflow run /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sarek \
    -profile pdc_kth \
    -name $1 \
    -params-file /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/$2 \
    --project=${COMPUTE_ACCOUNT} \
    --email=${USER_E_MAIL} \
    --step prepare_recalibration \
    --known_snps /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz \
    --known_snps_tbi /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi
this one is throwing? 
* --known_sites: /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz
* --known_sites_tbi: /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi
? just asking because of the 
sites
vs 
snps
mismatch
l
Let me check again, i think there might me 
_
and 
-
confusion in 
known-sites
UPDATE: can't run it due to some HPC system issues, will post an update ASAP.
I checked.
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nextflow run /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sarek \
    -profile pdc_kth \
    -name $1 \
    -params-file /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/$2 \
    --project=${COMPUTE_ACCOUNT} \
    --email=${USER_E_MAIL} \
    --step prepare_recalibration \
    --known_sites /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz \
    --known_sites_tbi /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi
is throwing
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* --known_sites: /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz
* --known_sites_tbi: /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi
r
odd, i'll take a look tomorrow
l
I am trying now with the run command below, using 
--known_indels
. Isn't this equivalent to 
--known_sites
in most cases? In any case, many thanks for your support!
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nextflow run /cfs/klemming/projects/snic/sllstore2017078/lech/clones/sarek \
    -profile pdc_kth \
    -name $1 \
    -params-file /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/$2 \
    --project=${COMPUTE_ACCOUNT} \
    --email=${USER_E_MAIL} \
    --step prepare_recalibration \
    --known_indels /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz
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