Merge pull request #13 from heuermh/add-seqkit-stats

Add nf-core seqkit/stats module

Author: olgabot

CHANGELOG.md

@@ -9,6 +9,8 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 
 ### `Added`
 
+- [[PR #13](https://github.com/nf-core/proteinannotator/pull/13)] Add nf-core seqkit/stats module
+
 ### `Fixed`
 
 ### `Dependencies`

conf/modules.config

@@ -27,4 +27,7 @@ process {
         ]
     }
 
+    withName: SEQKIT_STATS {
+        ext.args = ' ' // turn off --all default argument
+    }
 }

docs/output.md

@@ -13,6 +13,7 @@ The directories listed below will be created in the results directory after the
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
+- [SeqKit stats](#seqkit_stats) - Simple statistics for protein FASTA files
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
 ### MultiQC
@@ -31,6 +32,18 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 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>.
 
+### SeqKit stats
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `seqkit/`
+  - `{prefix}.tsv`: output of `seqkit stats` command on `{prefix}.fasta` input file, in tab-delimited text format.
+
+</details>
+
+[SeqKit stats](https://bioinf.shenwei.me/seqkit/usage/#stats) generates simple statistics for protein FASTA files, such as number of residues, minimal sequence length, average sequence length, and maximal sequence length.
+
 ### Pipeline information
 
 <details markdown="1">

modules.json

@@ -9,6 +9,11 @@
                         "branch": "master",
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
+                    },
+                    "seqkit/stats": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
                     }
                 }
             },