diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index f8707f63..2ac5826b 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -15,9 +15,6 @@ jobs:
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v2
- # TODO nf-core: You can customise AWS full pipeline tests as required
- # Add full size test data (but still relatively small datasets for few samples)
- # on the `test_full.config` test runs with only one set of parameters
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7663b023..1fdc453e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,12 @@
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).
+## [v2.2.4](https://github.com/nf-core/smrnaseq/releases/tag/2.2.4) - 2023-09-07
+
+- Update template to 2.10
+- Bugfix for issue with mirdeep2 channels [#289](https://github.com/nf-core/smrnaseq/issues/289)
+- Bugfix for issue with handling malformed GFF3 from mirbase (was forgotten in 2.2.3)
+
## [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
diff --git a/README.md b/README.md
index 20f9e247..7c010c00 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
#  
[](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+CI%22)
-[](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+linting%22)[](https://nf-co.re/smrnaseq/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
+[](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+linting%22)
[](https://nf-co.re/smrnaseq/results)[](https://doi.org/10.5281/zenodo.3456879)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 71a77e0b..74c7de72 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,9 +1,7 @@
report_comment: >
-
- This report has been generated by the nf-core/smrnaseq
+ This report has been generated by the nf-core/smrnaseq
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
-
+ documentation.
report_section_order:
"nf-core-smrnaseq-methods-description":
order: -1000
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 96bf1394..94077cd4 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -67,8 +67,8 @@ def check_samplesheet(file_in, file_out):
# Check valid number of columns per row
if len(lspl) != len(header):
print_error(
- "Invalid number of columns: found {} columns (header has {})".format(
- line_number, len(lspl), len(header)
+ "Invalid number of columns found - header has {} columns, content has {}. Number of rows {})".format(
+ len(header), len(lspl), line_number
),
f"Line #{line_number+2}",
line,
diff --git a/modules/local/mirdeep2_run.nf b/modules/local/mirdeep2_run.nf
index e4e2aaaf..26635a4f 100644
--- a/modules/local/mirdeep2_run.nf
+++ b/modules/local/mirdeep2_run.nf
@@ -10,10 +10,10 @@ process MIRDEEP2_RUN {
'biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
input:
- tuple val(meta2), path(fasta)
+ path(fasta)
tuple path(reads), path(arf)
- path hairpin
- path mature
+ tuple val(meta2), path(hairpin)
+ tuple val(meta2), path(mature)
output:
path 'result*.{bed,csv,html}', emit: result
diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index cc8d29a7..e97d6a09 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -24,9 +24,12 @@ process MIRTOP_QUANT {
script:
def filter_species = params.mirgenedb ? params.mirgenedb_species : params.mirtrace_species
"""
- mirtop gff --hairpin $hairpin --gtf $gtf -o mirtop --sps $filter_species ./bams/*
- mirtop counts --hairpin $hairpin --gtf $gtf -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
- mirtop export --format isomir --hairpin $hairpin --gtf $gtf --sps $filter_species -o mirtop mirtop/mirtop.gff
+ #Cleanup the GTF if mirbase html form is broken
+ GTF="$gtf"
+ sed 's/>/>/g' \$GTF | sed 's#
#\\n#g' | sed 's###g' | sed 's###g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${GTF}_html_cleaned.gtf
+ mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.gtf -o mirtop --sps $filter_species ./bams/*
+ mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.gtf -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
+ mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.gtf --sps $filter_species -o mirtop mirtop/mirtop.gff
mirtop stats mirtop/mirtop.gff --out mirtop/stats
mv mirtop/stats/mirtop_stats.log mirtop/stats/full_mirtop_stats.log
diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf
index 2649ebc1..a0bbc75e 100644
--- a/modules/local/parse_fasta_mirna.nf
+++ b/modules/local/parse_fasta_mirna.nf
@@ -25,7 +25,7 @@ process PARSE_FASTA_MIRNA {
gunzip -f \$FASTA
FASTA=\${FASTA%%.gz}
fi
- sed 's/>/>/g' \$FASTA | sed 's#
#\\n#g' | sed 's#
##g' | sed 's###g' > \${FASTA}_html_cleaned.fa
+ sed 's/>/>/g' \$FASTA | sed 's#
#\\n#g' | sed 's#
##g' | sed 's###g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${FASTA}_html_cleaned.fa
# Remove spaces from miRBase FASTA files
sed '#^[^>]#s#[^AUGCaugc]#N#g' \${FASTA}_html_cleaned.fa > \${FASTA}_parsed.fa
diff --git a/nextflow.config b/nextflow.config
index aa0e58e3..757e2f91 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -287,7 +287,7 @@ manifest {
description = """Small RNA-Seq Best Practice Analysis Pipeline."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '2.2.3'
+ version = '2.2.4dev'
doi = ''
}