Merge pull request sanger-tol#108 from tkchafin/1.3.0

Version 1.3.0 pre-release
tkchafin · Aug 22, 2024 · 1f1f240 · 1f1f240
2 parents 1b91ed8 + a31b253
commit 1f1f240
Show file tree

Hide file tree

Showing 32 changed files with 963 additions and 892 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -14,6 +14,7 @@ lint:
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
+    - tower.yml
   files_unchanged:
     - LICENSE
     - .github/CONTRIBUTING.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,25 +1,44 @@
-# nf-core/readmapping: Changelog
+# sanger-tol/readmapping: Changelog
 
 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).
 
-## [[1.3.0](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-06-XX]
+## [[1.3.0](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-08-23]
 
 ### Enhancements & fixes
 
 - Combined steps to improve the efficiency of the pipeline, especially on large genomes
 - "crumble" is now run on _every_ data type, not just PacBio
+- Added options for output format and to turn on/off crumble compression (https://github.com/sanger-tol/readmapping/pull/107)
+- Added `fastq` as possible input type for PacBio (https://github.com/sanger-tol/readmapping/pull/106) and Illumina/HiC (https://github.com/sanger-tol/readmapping/pull/96)
+- Disabled running `bwa index` when no short-read data provided (https://github.com/sanger-tol/readmapping/pull/100)
+- Added support for optional custom SAM header (https://github.com/sanger-tol/readmapping/pull/95)
+- Switch to `nf-validation` (https://github.com/sanger-tol/readmapping/pull/99) and further updates for nf-core v2.14 compliance (https://github.com/sanger-tol/readmapping/pull/98)
 
 ### Software dependencies
 
 Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
 
-| Dependency | Old version   | New version   |
-| ---------- | ------------- | ------------- |
-| `samtools` | 1.14 and 1.17 | 1.17 and 1.18 |
+| Dependency | Old version   | New version |
+| ---------- | ------------- | ----------- |
+| `blastn`   | 2.13          | 2.15        |
+| `minimap2` | 2.24          | 2.28        |
+| `samtools` | 1.14 and 1.17 | 1.20        |
+| `seqkit`   |               | 2.8.1       |
+| `seqtk`    |               | 1.4         |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
 
+### Parameters
+
+| Old parameter | New parameter  |
+| ------------- | -------------- |
+|               | '--header'     |
+|               | '--outfmt'     |
+|               | '--compression |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ## [[1.2.2](https://github.com/sanger-tol/readmapping/releases/tag/1.2.2)] - Norwegian Ridgeback (patch 2) - [2024-05-23]
 
 ### Enhancements & fixes
@@ -110,7 +129,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 
 ## [[v1.0.0](https://github.com/sanger-tol/readmapping/releases/tag/1.0.0)] – Ukrainian Ironbelly - [2022-05-19]
 
-Initial release of nf-core/readmapping, created with the [nf-core](https://nf-co.re/) template.
+Initial release of sanger-tol/readmapping, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,22 +1,42 @@
-# nf-core/readmapping: Citations
+# sanger-tol/readmapping: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
 > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
 
 ## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
 
-> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+>
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [Blast](https://pubmed.ncbi.nlm.nih.gov/20003500/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+  > Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PMID: 20003500; PMCID: PMC2803857.
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+- [BWA-MEM2](https://ieeexplore.ieee.org/document/8820962)
 
-  > 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.
+  > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium. 2019 May;314–24. doi: 10.1109/IPDPS.2019.00041.
+
+- [CRUMBLE]
+
+  > Bonfield JK, McCarthy SA, Durbin R. Crumble: reference free lossy compression of sequence quality values. Bioinformatics. 2019 Jan;35(2):337-339. doi: 10.1093/bioinformatics/bty608. PubMed PMID: 29992288; PMCID: PMC6330002.
+
+- [Minimap2](https://pubmed.ncbi.nlm.nih.gov/34623391/)
+
+  > Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics. 2021 Oct 8;37(23):4572–4. doi: 10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391; PMCID: PMC8652018.
+
+- [Samtools](https://pubmed.ncbi.nlm.nih.gov/33590861/)
+
+  > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819.
+
+- [SeqKit]
+
+  > Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016 Oct 5;11(10):e0163962. doi: 10.1371/journal.pone.0163962. PubMed PMID: 27706213; PMCID: PMC5051824.
+
+- [Seqtk]
+
+  > Li H. Toolkit for processing sequences in FASTA/Q formats. GitHub Repository. 2012. https://github.com/lh3/seqtk. Accessed August 2024.
 
 ## Software packaging/containerisation tools
 
@@ -34,7 +54,7 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
-  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+  > Merkel, D. Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014 Mar;2014(239):2. doi: 10.5555/2600239.2600241.
 
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 

diff --git a/README.md b/README.md
@@ -53,7 +53,9 @@ We thank the following people for their extensive assistance in the development
 
 - [Matthieu Muffato](https://github.com/muffato) for the text logo
 - [Guoying Qi](https://github.com/gq1) for being able to run tests using Nf-Tower and the Sanger HPC farm
-- [Tyler Chafin](https://github.com/tkchafin) for maintenance and updates
+- [Tyler Chafin](https://github.com/tkchafin) for maintenance, updates, and code reviews
+- [Chau Duong](https://github.com/reichan1998) for updates and code reviews
+- [Sandra Babirye](https://github.com/SandraBabirye) for updates and code reviews
 
 ## Contributions and Support
 

diff --git a/assets/slackreport.json b/assets/slackreport.json
@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/readmapping ${version} - ${runName}",
+            "author_name": "sanger-tol/readmapping ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

diff --git a/modules.json b/modules.json
@@ -1,13 +1,13 @@
 {
-    "name": "nf-core/readmapping",
-    "homePage": "https://github.com/nf-core/readmapping",
+    "name": "sanger-tol/readmapping",
+    "homePage": "https://github.com/sanger-tol/readmapping",
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
                     "blast/blastn": {
                         "branch": "master",
-                        "git_sha": "4262a04142431275e54e1f4b413628a2201ed6e6",
+                        "git_sha": "583edaf97c9373a20df05a3b7be5a6677f9cd719",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -17,7 +17,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "3afb95b2e15fc4a2347470255a7ef654f650c8ec",
+                        "git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
                         "installed_by": ["modules"]
                     },
                     "crumble": {
@@ -30,24 +30,14 @@
                         "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
                         "installed_by": ["modules"]
                     },
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
-                        "installed_by": ["modules"]
-                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "e83b347b3e674de6bb1bb7bdf9b2674768c8e0fe",
-                        "installed_by": ["modules"]
-                    },
-                    "multiqc": {
-                        "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
@@ -62,12 +52,12 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
@@ -78,7 +68,7 @@
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {

diff --git a/modules/nf-core/blast/blastn/tests/main.nf.test b/modules/nf-core/blast/blastn/tests/main.nf.test