Add bwa #103
Add bwa #103
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relates to Replace minimap2 with another mapper for short-read data? #102
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Nice! Looks good, I just built a new container w/ the latest RUN conda install bwa=0.7.18 samtools=1.20 && conda clean -a--> so it matches the conda environment! If we can have this in |
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| script: | ||
| """ | ||
| INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'` |
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Isn't the index passed in as a parameter (db_index)? If you only want to strip off the .amb you can use something like:
index_root=${db_index%.amb}
(not tested)
see https://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_06_02
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The BWA processes are copied from nf-core 😇
The index process outputs a folder called bwa, and with this line, you find the folder. Maybe amb is BWA specific? 🤔
configs/node.config
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I know this is a Nextflow thing, but vertically aligning curly braces makes for unnecessarily larger diffs with meaningless changes. I'd consider it bad style but that's just me. I can ignore them in GitHub but it's more of a pain when using command line git (e.g. git blame especially).
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I've seen too much nf-core code lately 😅
https://nf-co.re/docs/contributing/code_editors_and_styling/harshil_alignment
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Great! I would like to test it “real live” on the data where I also saw such discrepancies between |
| bwa mem \\ | ||
| -t $task.cpus \\ | ||
| \$INDEX \\ | ||
| $input \\ |
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bwa mem does automatically take care of single-end or paired-end read input, or? So you just pass $input and then this will be either a SE FASTQ or two PE FASTQs, right?
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yes, for single-end, it would be one fastq file; for paired-end, $input would be foo_1.fastq foo_2.fastq (space-separated)
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Did you use |
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