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### Description of the bug
New error when running raredisease, "Missing fromPath parameter". Same error when running analysis-type wgs or wes and same error when running locally or via nf-core.
Th…
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toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c
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## Bug report
Intermittently some of our processes appear to hang when running using the Google Lifesciences executor.
The Nextflow step appears to be hanging in the `nf-*-stage` action step wh…
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### Description of the bug
Error "No such variable: case_info " when running raredisease as well as a warning "A process with name 'PICARD_COLLECTWGSMETRICS_Y' is defined more than once in module scr…
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https://mp.weixin.qq.com/s/XQITfdnS6Zn6iTBtuladPw
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When the mean coverage is below 0.05X, the general stats table only shows 0.0X
For low coverage data an increase in significance would be helpful.
When mean coverage is 0.02495, I'd like to se…
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## COMPLETED
- [x] abacas (assigned @drpatelh)
- [x] agrvate (assigned @drpatelh)
- [x] bandage/image (assigned @drpatelh)
- [x] bismark/align (assigned @drpatelh)
- [x] bismark/deduplicat…
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Hi Dr. Cullen,
While running a Snakemake pipeline on a cluster environment, I encountered an error during the execution of the fastqs_to_ubam rule. This rule uses the gatk FastqToSam tool to conver…
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## bamQC-nf v1.0 workflow has the following:
### Steps
- [x] Validate cohort input file
- [x] samtools stats
- [x] mosdepth
- [x] qualimap bamqc
### Software
- [x] Singularity running Docker co…
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### Description of feature
Dear Serak developer,
I have tumor-normal pair bam files, and would like to only do a BAM file QC analysis (without any variant calling process). Is that possible for a…