ghga-de / nf-snvcalling Goto Github PK
View Code? Open in Web Editor NEWa Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
License: MIT License
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
License: MIT License
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fix input_checking.nf check nf-aceseq pipeline
implement nf-validation plugin
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install prettier for CI/CD checks
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There will be options for annotations to use with VEP
add VEP module
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Rearrange source requirements
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Current version is not actual vcf formatted.
Use use https://github.com/DKFZ-ODCF/SNVCallingWorkflow/blob/master/resources/analysisTools/snvPipeline/convertToStdVCF.py to output proper VCF to output proper vcf
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CI/CD integration needs to be ready for SNV calling phase.
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The reference set bundle which is used in PCAWG study can be found and downloaded here. (NOTE: only in hg19)
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Raw VCF output should be sorted.
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nextflow_schema.json missises some parameters
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GREP_SAMPLENAME takes input paths from path., this might be creating errors when one uses hidden paths.
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I have used nfcore-download command as suggested to pull the singularity images. But resulted in errors (see terminal outputs)
$nf-core download ghga-de/nf-snvcalling
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.14.1 - https://nf-co.re
WARNING Could not find GitHub authentication token. Some API requests may fail.
? Select release / branch: v2.0.0 [release]
? Include the nf-core's default institutional configuration files into the download? Yes
In addition to the pipeline code, this tool can download software containers.
? Download software container images: singularity
If you are working on the same system where you will run Nextflow, you can amend the downloaded images to the ones in the$NXF_SINGULARITY_CACHEDIR folder, Nextflow will
automatically find them. However if you will transfer the downloaded files to a different system then they should be copied to the target folder.
? Copy singularity images from $NXF_SINGULARITY_CACHEDIR to the target folder or amend new images to the cache? amend
If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
? Choose compression type: tar.gz
INFO Saving 'ghga-de/nf-snvcalling'
Pipeline revision: 'v2.0.0'
Use containers: 'singularity'
Container library: 'quay.io'
Using $NXF_SINGULARITY_CACHEDIR': /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image'
Output file: 'ghga-de-nf-snvcalling_v2.0.0.tar.gz'
Include default institutional configuration: 'True'
INFO Downloading centralised configs from GitHub
INFO Downloading workflow files from GitHub
INFO Processing workflow revision v2.0.0, found 8 container images in total.
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62% • 5/8 completed
kubran/bcftools:1.9 WARNING: SINGULARITY_CACHEDIR and APPTAINER_CACHEDIR have different values, using the latter ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ERROR "kubran/bcftools:1.9" failed for unclear reasons.
INFO Pulling of "kubran/bcftools:1.9" failed.
Please troubleshoot the command
"singularity pull --name /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-bcftools-1.9.img docker://quay.io/kubran/bcftools:1.9"
manually.
ERROR "kubran/bcftools:1.9" failed for unclear reasons.
ERROR Pulling of "kubran/bcftools:1.9" failed.
Please troubleshoot the command
"singularity pull --name /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-bcftools-1.9.img docker://quay.io/kubran/bcftools:1.9"
manually.
ERROR Not able to pull image of ('kubran/bcftools:1.9', '/omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-bcftools-1.9.img', None).
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 75% • 6/8 completed
kubran/odcf_mpileupsnvcalling:v0 WARNING: SINGULARITY_CACHEDIR and APPTAINER_CACHEDIR have different values, using the latter ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ERROR "kubran/odcf_mpileupsnvcalling:v0" failed for unclear reasons.
INFO Pulling of "kubran/odcf_mpileupsnvcalling:v0" failed.
Please troubleshoot the command
"singularity pull --name /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-odcf_mpileupsnvcalling-v0.img
docker://quay.io/kubran/odcf_mpileupsnvcalling:v0" manually.
ERROR "kubran/odcf_mpileupsnvcalling:v0" failed for unclear reasons.
ERROR Pulling of "kubran/odcf_mpileupsnvcalling:v0" failed.
Please troubleshoot the command
"singularity pull --name /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-odcf_mpileupsnvcalling-v0.img
docker://quay.io/kubran/odcf_mpileupsnvcalling:v0" manually.
ERROR Not able to pull image of ('kubran/odcf_mpileupsnvcalling:v0',
'/omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-odcf_mpileupsnvcalling-v0.img', None). Service might be down or internet
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━ 88% • 7/8 completed
kubran/samtools:v1.9 WARNING: SINGULARITY_CACHEDIR and APPTAINER_CACHEDIR have different values, using the latter ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ERROR "kubran/samtools:v1.9" failed for unclear reasons.
INFO Pulling of "kubran/samtools:v1.9" failed.
Please troubleshoot the command
"singularity pull --name /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-samtools-v1.9.img
docker://quay.io/kubran/samtools:v1.9" manually.
ERROR "kubran/samtools:v1.9" failed for unclear reasons.
ERROR Pulling of "kubran/samtools:v1.9" failed.
Please troubleshoot the command
"singularity pull --name /omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-samtools-v1.9.img
docker://quay.io/kubran/samtools:v1.9" manually.
ERROR Not able to pull image of ('kubran/samtools:v1.9', '/omics/groups/OE0526/internal/users/pritam/raredisease/singularity_image/kubran-samtools-v1.9.img', None).
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% • 8/8 completed
INFO Compressing output into archive
INFO Command to extract files: tar -xzf ghga-de-nf-snvcalling_v2.0.0.tar.gz
INFO MD5 checksum for 'ghga-de-nf-snvcalling_v2.0.0.tar.gz': f5abf45510cc5c85827e4e02597d0a65
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Nextflow version 23.10.1
DKFZ Cluster
Singularity
CenOS
fix versioning in pipeline
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fix documents
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generate test annotation files for full test case run
subtract regions in testdata.
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