From c8e225051c8cc1f3861d6c4028c01e3c0e8b2445 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Wed, 6 Sep 2023 19:57:45 +0000
Subject: [PATCH 01/15] Also clean up GFF

---
 modules/local/mirtop_quant.nf | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index cc8d29a7..3eed97dc 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -24,9 +24,11 @@ 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
+    sed 's/&gt;/>/g' \$gtf | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${gtf}_html_cleaned.fa
+    mirtop gff --hairpin $hairpin --gtf \${gtf}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
+    mirtop counts --hairpin $hairpin --gtf \${gtf}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
+    mirtop export --format isomir --hairpin $hairpin --gtf \${gtf}_html_cleaned.fa --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
 

From 25adf7979dba7918ffa88c7ce162b465b8d1c335 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 7 Sep 2023 12:21:10 +0000
Subject: [PATCH 02/15] Push fix

---
 modules/local/mirtop_quant.nf | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index 3eed97dc..e15ce9e3 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -25,10 +25,11 @@ process MIRTOP_QUANT {
     def filter_species = params.mirgenedb ? params.mirgenedb_species : params.mirtrace_species
     """
     #Cleanup the GTF if mirbase html form is broken
-    sed 's/&gt;/>/g' \$gtf | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${gtf}_html_cleaned.fa
-    mirtop gff --hairpin $hairpin --gtf \${gtf}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
-    mirtop counts --hairpin $hairpin --gtf \${gtf}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
-    mirtop export --format isomir --hairpin $hairpin --gtf \${gtf}_html_cleaned.fa --sps $filter_species -o mirtop mirtop/mirtop.gff
+    GTF="$gtf"
+    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${GTF}_html_cleaned.fa
+    mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
+    mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
+    mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa --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
 

From c6c3ff90285f8feca0052e153989cedef9fcf148 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 7 Sep 2023 13:06:02 +0000
Subject: [PATCH 03/15] Bump version and changelog

---
 CHANGELOG.md              | 3 +++
 assets/multiqc_config.yml | 4 ++--
 nextflow.config           | 2 +-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7663b023..62acd27c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,9 @@
 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
+
+- 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/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 8490cf0f..d2bfd50f 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.3" target="_blank">nf-core/smrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.4" 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/2.2.3/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/smrnaseq/2.2.4/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-smrnaseq-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 8ce36712..059feffe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -272,7 +272,7 @@ manifest {
     description     = """Small RNA-Seq Best Practice Analysis Pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '2.2.3'
+    version = '2.2.4'
     doi             = ''
 }
 

From 0ab71aed2e8e4e2d0ac2b2529a1331ee843a4ad0 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Thu, 7 Sep 2023 13:06:16 +0000
Subject: [PATCH 04/15] Prettier

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 62acd27c..cbc0610e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [v2.2.4](https://github.com/nf-core/smrnaseq/releases/tag/2.2.4) - 2023-09-07
 
 - 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

From 0d6aeef2453f59dc46965c9a4985e076bc7da408 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 8 Sep 2023 10:03:01 +0000
Subject: [PATCH 05/15] More sed magic

---
 modules/local/mirtop_quant.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index e15ce9e3..2d23c347 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -26,7 +26,7 @@ process MIRTOP_QUANT {
     """
     #Cleanup the GTF if mirbase html form is broken
     GTF="$gtf"
-    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${GTF}_html_cleaned.fa
+    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\n*$/{$d;N;};/\n$/ba' > \${GTF}_html_cleaned.fa
     mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
     mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
     mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa --sps $filter_species -o mirtop mirtop/mirtop.gff

From d33232da43ad2570e46c4df0ef2e785c7847a368 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 8 Sep 2023 10:09:24 +0000
Subject: [PATCH 06/15] Proper exiting of variables in sed expression ...

---
 modules/local/mirtop_quant.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index 2d23c347..905c1761 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -26,7 +26,7 @@ process MIRTOP_QUANT {
     """
     #Cleanup the GTF if mirbase html form is broken
     GTF="$gtf"
-    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\n*$/{$d;N;};/\n$/ba' > \${GTF}_html_cleaned.fa
+    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\n*\$/{\$d;N;};/\n\$/ba' > \${GTF}_html_cleaned.fa
     mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
     mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
     mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa --sps $filter_species -o mirtop mirtop/mirtop.gff

From ce3894a8e6a9e02c60a6f568dc7c8d22efe590c9 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 8 Sep 2023 11:59:51 +0000
Subject: [PATCH 07/15] Hopefully fix

---
 modules/local/mirtop_quant.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index 905c1761..82d06fad 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -26,7 +26,7 @@ process MIRTOP_QUANT {
     """
     #Cleanup the GTF if mirbase html form is broken
     GTF="$gtf"
-    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\n*\$/{\$d;N;};/\n\$/ba' > \${GTF}_html_cleaned.fa
+    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${GTF}_html_cleaned.fa
     mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
     mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
     mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa --sps $filter_species -o mirtop mirtop/mirtop.gff

From 53c0608e369ec7c4a9087aef4f9ebbfa3b2a332e Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Fri, 8 Sep 2023 18:47:04 +0000
Subject: [PATCH 08/15] Remove trailing newlines in FastA too

---
 modules/local/parse_fasta_mirna.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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/&gt;/>/g' \$FASTA | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${FASTA}_html_cleaned.fa
+    sed 's/&gt;/>/g' \$FASTA | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##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
 

From 263fb6234cf2f2f502c3284f84e80b5e5deb4302 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 11 Sep 2023 08:51:42 +0000
Subject: [PATCH 09/15] Cleaned up

---
 modules/local/mirtop_quant.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index 82d06fad..90bdfc1d 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -26,9 +26,9 @@ process MIRTOP_QUANT {
     """
     #Cleanup the GTF if mirbase html form is broken
     GTF="$gtf"
-    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${GTF}_html_cleaned.fa
-    mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
-    mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
+    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##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.fa --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

From c65dc160a542f6136ac9163dab87ed5260fea1c6 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 11 Sep 2023 10:01:22 +0000
Subject: [PATCH 10/15] Fix for mirTop

---
 modules/local/mirtop_quant.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
index 90bdfc1d..e97d6a09 100644
--- a/modules/local/mirtop_quant.nf
+++ b/modules/local/mirtop_quant.nf
@@ -29,7 +29,7 @@ process MIRTOP_QUANT {
     sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##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.fa --sps $filter_species -o mirtop 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
 

From 21b10e98836f6a671709d3a0437e0f3905651955 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 11 Sep 2023 10:15:26 +0000
Subject: [PATCH 11/15] Add suggestions by @mdozmorov

---
 bin/check_samplesheet.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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,

From 963b02ee7e289e5b05906ab0d8e89612fc61990b Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lpantano@nextrna.com>
Date: Thu, 19 Oct 2023 13:31:54 -0400
Subject: [PATCH 12/15] fix input for mirdeep2 run

---
 modules/local/mirdeep2_run.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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

From b2b3d9984e424d44f6c3bb1da42310d44c36f873 Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lpantano@nextrna.com>
Date: Fri, 20 Oct 2023 16:15:05 -0400
Subject: [PATCH 13/15] fix some lint warnings

---
 .github/workflows/awsfulltest.yml | 3 ---
 CHANGELOG.md                      | 2 ++
 README.md                         | 2 +-
 3 files changed, 3 insertions(+), 4 deletions(-)

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 cbc0610e..1fdc453e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [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
diff --git a/README.md b/README.md
index 20f9e247..7c010c00 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # ![nf-core/smrnaseq](docs/images/nf-core-smrnaseq_logo_light.png#gh-light-mode-only) ![nf-core/smrnaseq](docs/images/nf-core-smrnaseq_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3456879-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3456879)
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
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From 256da50f4193f2b5736f2b42e80d764c775b661a Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 23 Oct 2023 11:06:14 +0000
Subject: [PATCH 14/15] Hopefully fixing last lint error

---
 assets/multiqc_config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index d2bfd50f..74c7de72 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.4" target="_blank">nf-core/smrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/releases/tag/dev" 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/2.2.4/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/smrnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-smrnaseq-methods-description":
     order: -1000

From 4c27e8cc8f3d46b1470bcb93416d42c48dca9cfd Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 23 Oct 2023 11:08:20 +0000
Subject: [PATCH 15/15] Missing dev statement towards dev branch

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 68753af8..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         = '2.2.4'
+    version = '2.2.4dev'
     doi             = ''
 }