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remove space in genome header and special nt in hairpin for mirdeep2 … #79

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merged 9 commits into from
May 10, 2021
Merged

remove space in genome header and special nt in hairpin for mirdeep2 … #79

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ad2ff33
remove space in genome header and special nt in hairpin for mirdeep2 …
sdjebali May 4, 2021
58f6b68
adding changes made to CHANGELOG.md
sdjebali May 4, 2021
e750145
Revert to use a perl regex, but with additional characters
ewels May 6, 2021
9a5774f
Merge upstream changes, fix conflicts
ewels May 6, 2021
111acd5
lint generated files
sdjebali May 6, 2021
0c4c64b
Merge branch 'dev' of https://github.com/sdjebali/smrnaseq into dev
sdjebali May 6, 2021
20c8279
remove spaces in genome headers
sdjebali May 7, 2021
b3354e7
Update CHANGELOG.md
KevinMenden May 10, 2021
d632153
Update CHANGELOG.md
KevinMenden May 10, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,7 @@

## v1.1dev - [date]

* remove spaces in genome headers and replace special nt by N in hairpin file for mirdeep2 to work. Follow up from [[#69]] (https://github.com/nf-core/smrnaseq/pull/79)
* Accept custom genome and remove non-canonical letters in the genome. Thanks to @sdjebali. Follow up from [[#63]](https://github.com/nf-core/smrnaseq/pull/63)
* Fix error when only one sample is in the input [[#31]](https://github.com/nf-core/smrnaseq/issues/31)
* Change `--reads` to `--input` for consistency with rest of nf-core
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4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -840,15 +840,15 @@ process mirdeep2 {

script:
"""
perl -ane 's/y/N/ig;print;' $hairpin > hairpin_yn.fa
awk '{ gsub(/Y/,"N",\$0); gsub(/B/,"N",\$0); gsub(/K/,"N",\$0); gsub(/M/,"N",\$0); gsub(/R/,"N",\$0); gsub(/S/,"N",\$0); gsub(/W/,"N",\$0); print}' $hairpin > hairpin_ok.fa
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I think you're just adding other nucleotides beyond Y here, right? Is there a reason that we can't just do:

perl -ane 's/[ybkmrsw]/N/ig;print;' $hairpin > hairpin_yn.fa

I'd be inclined to use this type of command instead as it's a lot more succinct / easy to read and also case-insensitive..

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Also I'm not sure I see where you are removing spaces in the headers? Am I missing that somewhere?

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thanks for having a look

I am fine with the perl command instead of mine but maybe use a different name for the output file as we do not only remove Y nt

I am removing spaces in headers for the genome file, not the hairpin file, it is at another location in the code

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I am removing spaces in headers for the genome file, not the hairpin file, it is at another location in the code

Right, that's what I was wondering - but I can't see that in this pull request, right?

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I have now added the actual command to remove spaces in genome headers


miRDeep2.pl \\
$reads_collapsed \\
$refgenome \\
$reads_vs_refdb \\
$mature \\
none \\
hairpin_yn.fa \\
hairpin_ok.fa \\
-d \\
-z _${reads_collapsed.simpleName}
"""
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