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Patch Release PR 2.2.3 #280

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merged 8 commits into from
Sep 6, 2023
Merged

Patch Release PR 2.2.3 #280

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884cdad
Bump versions + fix 271
apeltzer Sep 5, 2023
4f93a99
Fixing tests
apeltzer Sep 5, 2023
6ebe3d5
Attempt at fixing HTML tags from downloading
apeltzer Sep 6, 2023
2308518
Expression for newline was incorrect
apeltzer Sep 6, 2023
6f79a99
Prettier
apeltzer Sep 6, 2023
d42cfef
Update CHANGELOG.md
apeltzer Sep 6, 2023
87a6f68
Merge pull request #279 from nf-core/fix-271
apeltzer Sep 6, 2023
a3ed96d
Bump to 2.2.3
apeltzer Sep 6, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,10 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [v2.2.3](https://github.com/nf-core/smrnaseq/releases/tag/2.2.3) - 2023-09-06

- [[#271]](https://github.com/nf-core/smrnaseq/issues/271) - Bugfix for parsing hairpin and mature fasta files

## [v2.2.2](https://github.com/nf-core/smrnaseq/releases/tag/2.2.2) - 2023-09-04

- [[#253]](https://github.com/nf-core/smrnaseq/pull/253) - Remove globs from process alias when using ECR containers
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.2" target="_blank">nf-core/smrnaseq</a>
This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.3" target="_blank">nf-core/smrnaseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/smrnaseq/2.2.2/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/smrnaseq/2.2.3/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-smrnaseq-methods-description":
order: -1000
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6 changes: 3 additions & 3 deletions conf/test.config
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Expand Up @@ -23,9 +23,9 @@ params {

input = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/samplesheet/v2.0/samplesheet.csv'
fasta = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa'
mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa'
hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa'
mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3'
mature = 'https://mirbase.org/download/CURRENT/mature.fa'
hairpin = 'https://mirbase.org/download/CURRENT/hairpin.fa'
mirna_gtf = 'https://mirbase.org/download/hsa.gff3'
mirtrace_species = 'hsa'
protocol = 'illumina'
skip_mirdeep = true
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5 changes: 2 additions & 3 deletions modules/local/parse_fasta_mirna.nf
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Expand Up @@ -25,10 +25,9 @@ process PARSE_FASTA_MIRNA {
gunzip -f \$FASTA
FASTA=\${FASTA%%.gz}
fi
sed 's/&gt;/>/g' \$FASTA | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${FASTA}_html_cleaned.fa
# Remove spaces from miRBase FASTA files
# sed -i 's, ,_,g' \$FASTA
sed '#^[^>]#s#[^AUGCaugc]#N#g' \$FASTA > \${FASTA}_parsed.fa
# TODO perl -ane 's/[ybkmrsw]/N/ig;print;' \${FASTA}_parsed_tmp.fa > \${FASTA}_parsed.fa
sed '#^[^>]#s#[^AUGCaugc]#N#g' \${FASTA}_html_cleaned.fa > \${FASTA}_parsed.fa

sed -i 's#\s.*##' \${FASTA}_parsed.fa
seqkit grep -r --pattern \".*${filter_species}-.*\" \${FASTA}_parsed.fa > \${FASTA}_sps.fa
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -272,7 +272,7 @@ manifest {
description = """Small RNA-Seq Best Practice Analysis Pipeline."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '2.2.2'
version = '2.2.3'
doi = ''
}

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