Adress issues from review

.github/workflows/ci.yml

@@ -15,6 +15,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   NFT_VER: "0.9.0"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
@@ -26,7 +28,7 @@ concurrency:
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}"
     runs-on: ubuntu-latest

.github/workflows/template_version_comment.yml

@@ -10,9 +10,11 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -24,20 +26,21 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #

.gitignore

@@ -6,5 +6,4 @@ results/
 testing/
 testing*
 *.pyc
-execution_trace*
-.nf-test*
+null/

.nf-core.yml

@@ -3,7 +3,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.fastp_known_mirna_adapters
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v2.4.0 - 2024-10-07 - Navy Iron Boxer
+## v2.4.0 - 2024-10-14 - Navy Iron Boxer
 
 - [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347) - change conda-base to conda-forge channel.
 - [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347) - set python version to 3.7 to fix pysam issue.

CITATIONS.md

@@ -38,6 +38,7 @@
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 - [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/)

README.md

@@ -51,7 +51,7 @@ You can find numerous talks on the nf-core events page from various topics inclu
    4. ncRNA filtration
    5. piRNA filtration
    6. Others filtration
-5. UMI barcode deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools)) <!-- TODO, isn't this done on the UMI step above? -->
+5. UMI barcode deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
 6. miRNA quantification
    - EdgeR
      1. Reads alignment against miRBase mature miRNA ([`Bowtie1`](http://bowtie-bio.sourceforge.net/index.shtml))
@@ -82,7 +82,7 @@ You can test the pipeline as follows:
 
 ```bash
 nextflow run nf-core/smrnaseq \
-   -profile test \
+   -profile test,docker \
   --outdir <OUTDIR>
 ```
 

bin/collapse_mirtop.r

@@ -1,6 +1,6 @@
 #!/usr/bin/env Rscript
 
-# Written by Lorena Pantano and released under the MIT license.
+# Written by Lorena Pantano and released under the MIT license. See LICENSE https://github.com/nf-core/smrnaseq/blob/master/LICENSE for details.
 
 library(data.table)
 # Command line arguments

bin/edgeR_miRBase.r

@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 
 # Originally written by Phil Ewels and Chuan Wang and released under the MIT license.
-# Contributions by Alexander Peltzer, Anabella Trigila, James Fellows Yates, Sarah Djebali, Kevin Menden, Konrad Stawinski and Lorena Pantano also released under the MIT license.
+# Contributions by Alexander Peltzer, Anabella Trigila, James Fellows Yates, Sarah Djebali, Kevin Menden, Konrad Stawinski and Lorena Pantano also released under the MIT license. See LICENSE https://github.com/nf-core/smrnaseq/blob/master/LICENSE for details.
 
 # Command line arguments
 args = commandArgs(trailingOnly=TRUE)

conf/test_contamination_tech_reps.config

@@ -25,10 +25,10 @@ params {
     skip_mirdeep             = true
     skip_fastqc              = true
 
-    filter_contamination = true
-    cdna                 = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.cdna.all.fa"
-    ncrna                = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.ncrna.fa"
-    trna                 = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/hg19-tRNAs.fa"
+    filter_contamination     = true
+    cdna                     = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.cdna.all.fa"
+    ncrna                    = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/Homo_sapiens.GRCh37.ncrna.fa"
+    trna                     = "https://huggingface.co/datasets/nf-core/smrnaseq/resolve/main/GRCh37/hg19-tRNAs.fa"
 }
 
 // Include illumina config to run test without additional profiles

conf/test_nextflex.config

@@ -22,8 +22,8 @@ params {
     mirna_gtf           = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3'
     mirtrace_species    = 'hsa'
 
-    skip_mirdeep             = true
-    save_intermediates       = true
+    skip_mirdeep        = true
+    save_intermediates  = true
     //skip_fastp // this profile should not be used with skip_fastq to allow for testing paired end sample handling
 
 }

modules.json

@@ -8,8 +8,7 @@
                     "bioawk": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/bioawk/bioawk.diff"
+                        "installed_by": ["modules"]
                     },
                     "blat": {
                         "branch": "master",
@@ -49,7 +48,7 @@
                     "fastp": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "fastqc": {
                         "branch": "master",
@@ -98,33 +97,33 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["bam_stats_samtools", "modules"]
+                        "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["bam_stats_samtools", "modules"]
+                        "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["bam_sort_stats_samtools", "modules"]
+                        "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["bam_sort_stats_samtools", "modules"]
+                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
+                        "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["bam_stats_samtools", "modules"]
+                        "installed_by": ["bam_stats_samtools"]
                     },
                     "seqcluster/collapse": {
                         "branch": "master",
@@ -139,8 +138,7 @@
                     "seqkit/grep": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/seqkit/grep/seqkit-grep.diff"
+                        "installed_by": ["modules"]
                     },
                     "seqkit/replace": {
                         "branch": "master",
@@ -155,7 +153,7 @@
                     "umitools/extract": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "untar": {
                         "branch": "master",
@@ -193,12 +191,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {