DRAFT: Update nf-core-modules 2 #686
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asp8200
commented
Jul 25, 2022
| @@ -1000,7 +1000,7 @@ workflow SAREK { | |||
| ch_versions = ch_versions.mix(TUMOR_ONLY_VARIANT_CALLING.out.versions) | |||
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| //QC | |||
| VCF_QC(vcf_to_annotate, intervals_bed_combined) | |||
| VCF_QC(vcf_to_annotate, TUMOR_ONLY_VARIANT_CALLING.out.manta_vcf_tbi, intervals_bed_combined) | |||
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I know that command only works for the test for manta-tumor-only. I guess one would have to do something like the "mixed" vcf_to_annotate for the tbi-files.
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maxulysse
reviewed
Jul 26, 2022
| target_bed | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| BCFTOOLS_STATS(vcf) | ||
| BCFTOOLS_STATS(vcf, tbi, target_bed) |
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Suggested change
| BCFTOOLS_STATS(vcf, tbi, target_bed) | |
| BCFTOOLS_STATS(vcf, []) |
I would try just this actually
maxulysse
reviewed
Jul 26, 2022
| @@ -9,6 +9,8 @@ process BCFTOOLS_STATS { | |||
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| input: | |||
| tuple val(meta), path(vcf) | |||
| tuple val(meta), path(vcf_tbi) | |||
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Why suggesting changes in the modules?
SusiJo
reviewed
Jul 26, 2022
| @@ -9,6 +9,8 @@ process BCFTOOLS_STATS { | |||
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| input: | |||
| tuple val(meta), path(vcf) | |||
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Suggested change
| tuple val(meta), path(vcf) | |
| tuple val(meta), path(vcf), path(tbi) |
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Let's keep the naming as in the other modules (i.e. bcftools/consensus).
When everything is working please update the bcftools/stats module upstream.
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I had also thought about trying out sth like this to find the right index file in the script section:
INDEX=find -L ./ -name "${prefix}.vcf.tbi"`` and then passing the \$INDEX to the `bcftools/stats` command, but i could not get it to run due to nextflow/bash problems.
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@maxulysse : I'm including the tbi-file in the input of the module bcftools/stats because, without it, the following test
nextflow run main.nf -profile test,tools_tumoronly,singularity --tools manta
resulted in the following error:
Process `NFCORE_SAREK:SAREK:VCF_QC:BCFTOOLS_STATS (sample2)` terminated with an error exit status (255)
Command executed:
bcftools stats \
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--regions-file multi_intervals.bed \
sample2.manta.tumor_sv.vcf.gz > sample2.manta.tumor_sv.bcftools_stats.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_QC:BCFTOOLS_STATS":
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS
Command exit status:
255
Command output:
(empty)
Command error:
[E::idx_find_and_load] Could not retrieve index file for 'sample2.manta.tumor_sv.vcf.gz'
Failed to read from sample2.manta.tumor_sv.vcf.gz: could not load index
Work dir:
/home/aspe/dev/fork_sarek/work/9b/0c3268ad4e17ee489871c6849292ff
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Hi @SusiJo and @maxulysse : Sorry about this mess and thanks a lot for all your comments and links to previous discussions. I'll take a careful look at it all. |
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@maxulysse and @SusiJo : If I just pass an empty list ( Is that an okay solution for you guys? @FriederikeHanssen mentioned that with the target-bed-file supplied for wes-samples, BCFTOOLS_STATS will produce a depth-plot: Perhaps we don't need that depth-plot for now? How about we just use an empty list ( |
Sounds ok enough.
OK for doing that in a separate PR |
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We are going for the solution in PR. |
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It seems that are some problems with getting Sarek to use the updated nf-core-modules, in particular,
BCFTOOLS_STATS. I made some changes in Sarek in order to get a vcf-tbi-file (for manta-tumor-only) toBCFTOOLS_STATS.With this PR, I got the following test working:
which was failing in the previous PR #685, however, before continuing with this approach, I'd like some feedback.
If this approach is usable, then it will have to be extended to get all the tests working.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).