Adjustments for #76 , rename certain options to be more explicit #81
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docs/usage.md
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| This can be used to only keep mapped reads for downstream analysis. By default turned off, all reads are kept in the BAM file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing. | ||
| This can be used to only keep mapped reads in the BAM file for downstream analysis. By default turned off, all reads are kept in the BAM file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing. |
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Maybe change following line to: 'By default turned off, where all reads are kept in the bam file.
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Generally looks good, made a minor suggestion for description. only think that isn't clear to me now is what if you want to discard unmapped reads entirely? Unless I misunderstand - I currently see only two cases: 1) where mapped and unmapped reads are retained but in separate BAMs and 2) where mapped and unmapped reads are in the same BAM. I am thinking for cases where people have storage space issues and want to minimise their data to stuff of interest. (This would be another issue, unless I have misunderstood) |
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I added an option that can remove the unrequired unmapped reads on user request. By default, its turned off, but of course can be turned on by users if they want to :-) Also added documentation on that @jfy133 let me know what you think .-) |
docs/usage.md
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| This can be used to only keep mapped reads for downstream analysis. By default turned off, all reads are kept in the BAM file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing. | ||
| This can be used to only keep mapped reads in the BAM file for downstream analysis. By default turned off, where all reads are kept in the bam file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing. |
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Possibly rephrase again for clarity (my bad):
Use only mapped reads in the BAM file for downstream analysis. Unmapped reads are stored in a separate BAM and FASTQ format e.g. for different downstream processing. By default turned off, where default behaviour is to keep both mapped and unmapped reads in the output BAM file.
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I wonder if it makes sense to instead have a independent flag to save unmapped reads in FASTQ rather than BAM format. In this case we will be make redundancy.
docs/usage.md
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| ### `--bam_discard_unmapped_entirely` | ||
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| This discards all unmapped and extracted reads entirely. By default, this is turned off. | ||
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| ### `--bam_keep_all` |
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What is the difference of this flag verses --bam_retain_all_reads?
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--bam_discard_unmapped_entirely
Removes the unmapped reads file only, the BAM file contains only mapped reads and unmapped reads are entirely discarded (no fastq/bam at all present).
I guess I'll have to give this another proper thought. Right now bam_retain_all_reads just is the thing to turn on BAM filtering in general.
This renames a couple of things to different names, to make sure people understand what these options mean.
cf #76
Namely:
bam_keep_mapped_only ==> bam_analyse_mapped_only
bam_filter_reads ==> bam_retain_all_reads
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedLearn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md