Seqkit

CHANGELOG.md

@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#59](https://github.com/nf-core/seqinspector/pull/59) Seqkit Stats TSV output.
 - [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools

CITATIONS.md

@@ -18,6 +18,10 @@
 
 > 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.
 
+- [Seqkit](https://doi.org/10.1371/journal.pone.0163962)
+
+> Wei Shen, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. [doi:10.1002/imt2.191](https://doi.org/10.1002/imt2.191).
+
 - [Seqtk](https://github.com/lh3/seqtk)
 
 ## Software packaging/containerisation tools

README.md

@@ -34,6 +34,7 @@
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+4. Provide Seqkit summary stats ([`SeqkitStats`](https://bioinf.shenwei.me/seqkit/usage/#stats))
 
 ## Usage
 

conf/modules.config

@@ -26,6 +26,10 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: SEQKIT_STATS {
+        ext.args = ''
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

docs/output.md

@@ -13,6 +13,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [SeqkitStats](#seqkitstats) - Per sample TSV file with summary statistics
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### Seqtk
@@ -72,6 +73,18 @@ nf-core/seqinspector will generate the following MultiQC reports:
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
+### SeqkitStats
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqkit/`
+  - `*.tsv`: Per sample TSV file with summary statistics.
+
+</details>
+
+[SeqkitStats](https://bioinf.shenwei.me/seqkit/usage/#stats) it gives simple statistics such as number of sequences, min/max_len, N50, Q20%, Q30% and GC%. For further reading and documentation see the [Seqkit help pages]([Seqkit help](https://bioinf.shenwei.me/seqkit/)).
+
 ### Pipeline information
 
 <details markdown="1">

modules.json

@@ -15,6 +15,11 @@
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
+                    "seqkit/stats": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",