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In DNACapture workflow, qc_summary_cohort_analysis job hangs instead of proceeding when all samples are finished with post alignment jobs. Most likely, this is due to mismatch between job log string a…
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- [x] fastp
- [x] bowtie2 index
- [x] bowtie2 align
- [x] snpeff
- [x] snpsift extractFields
- [x] samtools view
- [x] samtools mpileup
- [x] samtools faidx
- [x] ivar trim
- [x] picard coll…
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Hi,
Thanks for developing the tool. When I tried to run CNV_Radar.r, I recevied the followng error:
zip: tumor.unifiedGenotyper_5g.snpEFF.vcf.gz: No such file or directory
tumor.bqsr.unifiedGeno…
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I'm new to this tool. I tried running it on Mac. I had below the parameters:
```
sra: [SRR629563] # paired-end SRAs, comma separated, can leave empty, e.g. SRR629563
fq: [] # paired-end fastq p…
llniu updated
3 years ago
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https://mp.weixin.qq.com/s/tlAv3U6Xfu2Lq2v_RGK6nw
ixxmu updated
2 years ago
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## Bug report
Running the nf-core/sarek pipeline from a node with 128 Cores and 256 Threads, 1TB ram using Singularity and SGE.
Similar to https://github.com/nextflow-io/nextflow/issues/1871 and …
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A user has complained that the "SnpSift Filter" tool always fails. It seems to be because Java is missing.
`/data/part0/tmp/jobs/083/83088/tool_script.sh: 9: /data/part0/tmp/jobs/083/83088/tool_scr…
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Hi,
My understanding is that when snpEff is used with `-o gatk`, snpEff only reports the effect having the highest impact, something based on what the GATK team implemented.
My question is how…
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Hi,
1. I have 300 RNAseq raw files and I would like to use this pipeline to create a sample specific database for the downstream proteogenomics analysis. Could you help me with the commands which …