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**Describe the bug**
Seems that collection input with `multiple="true"` (ie ``) is possible but has some rough edges.
- its used in Galaxy tests: https://github.com/galaxyproject/galaxy/blob/dev…
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I am running piper with qualimap2, I check the output of qc under /06_final_alignment_qc and see that *.log, *.out, and *.done are created but no subdirectory for actual output. I went a head and reru…
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Hello Jianhong,
Thanks for your excellent work!
My bam file is so big that it costs a lot of resources during the running.
In order to reduce the time consumption, I tried to perform the analys…
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Whelp, I guess we have to tackle the bull.
First thoughts, we need to work out what nf-core/modules we would need, check what are already available and what we would have to write.
List based on…
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The existing [SARS-CoV-2 variant analysis] tutorial is focused on the analysis of metagenomic sequencing data. The majority of data being produced, however, uses the ARTIC amplicon protocol (for Illum…
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During my committee meeting it was decided that the number of variants used in my PCA was a little high for what we were expecting. Here I am going back through the SNP calling process to validate the…
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Java programs should set tmp dir and max memory:
```nextflow
script:
sample_name = vcf.baseName
mem = task.memory ? task.memory.toGiga() : task.cpus * 6
// Also optionally check…
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We will need to perform quality control on sequencing reads, `BAM` files generated by aligners and alignment statistics output by aligners.
Use the small `BAM` file provided at the following [link…
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Recently we ran into a situation where input bams were not generated by Tempo and the ID was `s_C_000184_T002_d` but the basename of the bam was `s_C_000184_T002_d___bqsr.bam`, causing failures or rec…
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See @bgruening comment and sample history here https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-289317874. It would seem to be unrelated to the original issue to me so I wanted to trac…